commit db2ad3e19068cbafde72ecde75d0638bbb3598ba Author: Heng Li Date: Thu Feb 16 14:45:17 2012 -0500 removed downsample.c commit 6c55c576903992c6fef148fe3b606fbc8bd10655 Author: Heng Li Date: Thu Feb 16 14:45:06 2012 -0500 print to output commit db1044a34e6049c87eaa63c39ed6e56f03e7d4c1 Author: Heng Li Date: Thu Feb 16 14:39:34 2012 -0500 removed sample Downsampling already exists in "view". View also keeps pairing while "sample" does not. commit ffdeed3e5d4a530bfdf6f9ba97fff0ba7add6cba Merge: 2daad7b accf026 Author: Heng Li Date: Thu Feb 16 14:22:15 2012 -0500 Merge branch 'master' of github.com:lh3/samtools commit accf0260fd1117e10047344345d40b31a9ec31bb Merge: 9134e0d c554160 Author: Heng Li Date: Thu Feb 16 11:21:14 2012 -0800 Merge pull request #8 from nh13/master Patches commit c554160df16ec7748cfdda4c7b54c641be7b809f Author: Nils Homer Date: Thu Feb 16 14:06:52 2012 -0500 * more README.md work commit 2a81ffe349208d917666808fbc9f3041e0cb57de Author: Nils Homer Date: Thu Feb 16 14:06:10 2012 -0500 * more README work commit fb3125f732715f62cded8685a23a002a96ce009b Author: Nils Homer Date: Thu Feb 16 14:05:19 2012 -0500 * more README work commit 444d41002c37e1c3d0f9208b4a88126c47276386 Author: Nils Homer Date: Thu Feb 16 14:02:13 2012 -0500 * updating README commit dec53cb1043fe7efadfde75fa2fd39b76de22e54 Author: Nils Homer Date: Thu Feb 16 13:55:01 2012 -0500 updating the README for markdown syntax commit 798da18c346dca8ec6005582a0ddb1d5420b04ca Author: Nils Homer Date: Thu Feb 16 13:48:35 2012 -0500 adding a README with the current differences between this repository and the official one commit 4d22d86c0f28636662f2144a88cd168e104c4275 Author: Nils Homer Date: Thu Feb 16 13:35:03 2012 -0500 adding "samtools sample" to the main commit 893c25a37c21005dc42f45d45e9ad78ddc5f29bb Author: Nils Homer Date: Thu Feb 16 13:33:51 2012 -0500 * removing some compile flags to work with OS X commit 7ac22f72fdc32edd5c24af6baebfa7db5faf8e7b Author: Jonathan Manning Date: Thu Feb 16 10:47:14 2012 -0500 Check write filehandle after opening for write. tamw/tamr is a union type, so change is only semantic. Signed-off-by: Nils Homer commit fef53330416631690f60fdff42b6e43d764170dc Author: Jonathan Manning Date: Thu Feb 16 10:44:59 2012 -0500 Catch and report invalid BAM header, instead of segfaulting later on. Signed-off-by: Nils Homer commit 5cc013fe4930bf9b6e7963aab1cd4a3c94f695bc Author: Jonathan Manning Date: Thu Feb 16 10:44:16 2012 -0500 Add downsample to examples. Signed-off-by: Nils Homer commit b3fa9e7071532905a81dc7aa48eadc24b8c8846b Author: Jonathan Manning Date: Thu Feb 16 10:43:48 2012 -0500 Adjust for leading hard clip on colorspace reads. Signed-off-by: Nils Homer commit 1a9296c1389469d1c1db5b8069f0e11ffcc8abb2 Author: Jonathan Manning Date: Thu Feb 16 10:42:52 2012 -0500 Add samtools sample command, contributed by Davide Cittaro . Signed-off-by: Nils Homer commit 2a804f3379748aeba944f1dec306dd726ff3235e Author: Jonathan Manning Date: Thu Feb 16 10:42:07 2012 -0500 Add samtools qa command, contributed by Roman Valls Guimera . Signed-off-by: Nils Homer commit 0f3207fe8fd93e44d40fcf57204079c8c06d24a6 Author: Jonathan Manning Date: Thu Feb 16 10:39:08 2012 -0500 Makefile cleanup - allow CC, CFLAGS, LDFLAGS to be passed on make command line. Use LDFLAGS in samtools compile. Signed-off-by: Nils Homer commit 6e7df604025f6a86881bf7f4a16f30e15d31538a Author: Jonathan Manning Date: Thu Feb 16 10:31:15 2012 -0500 Allow max_mem for sort to be specified with units. Signed-off-by: Nils Homer commit f12ebcaf6e60d34180a27d70e09b743cef140b98 Author: Jonathan Manning Date: Thu Feb 16 10:29:11 2012 -0500 Allow user defined [lowercase] tags in header elements. Signed-off-by: Nils Homer commit 50b931fa3312dc109537a4260698ddecd0f06a05 Author: Jonathan Manning Date: Thu Feb 16 10:27:11 2012 -0500 Check lowerbound in text entry box to avoid segfault in tview. Remove redundant call to bam_aux_get. Signed-off-by: Nils Homer commit 5e729da5190949a813d20d329eab7ddb661816bd Author: Nils Homer Date: Thu Feb 16 10:31:48 2012 -0500 * fixing overflow/underflow in integer parsing commit fa50a4330b9abedaf07c26e13d31f05e57f1d319 Author: Nils Homer Date: Thu Feb 16 10:30:40 2012 -0500 * updating help message for samtools depth commit 79e52c9624b6dd3bdfdf439f4b4bc6f774c230a4 Author: Nils Homer Date: Thu Feb 16 10:29:32 2012 -0500 * adding support for outputting a circos histogram file in "samtools depth". Use the "-c/-B" options. commit 2daad7b52daa86561c0fb65fe366691fad9f5ed3 Author: Heng Li Date: Thu Feb 16 09:31:57 2012 -0500 bugfix: wrong SP; missing DV in the VCF hdr commit 9134e0d5047c281ef3bd53da91771d4814a5131c Author: Heng Li Date: Wed Feb 8 11:19:12 2012 -0500 missing support of DV commit 34ebf12078c1d1015a0b8b9a9221243a60b22893 Author: Heng Li Date: Wed Feb 8 11:08:56 2012 -0500 new BCF DV format: number of variant reads commit 9589d3312fa2d076f48bdd68e2a5edd419c8070c Author: Heng Li Date: Tue Jan 10 10:30:27 2012 -0500 scale depth to quality (hidden option) commit 704473e14668333ecaca5fb7b238af405c43e3b1 Author: Heng Li Date: Tue Jan 10 10:18:17 2012 -0500 really nothing commit 01b307fd287962372bbf07461c88b54f41636817 Author: Heng Li Date: Wed Dec 7 13:07:42 2011 -0500 added an example containing 'B' commit c678791f0451ceb9205c1ab5c52c84641863c99a Author: Heng Li Date: Sat Dec 3 12:10:30 2011 -0500 'B' now moves backward w.r.t. the query commit 152119bc06a073933ca830e8e1407538e44626cc Author: Heng Li Date: Fri Dec 2 10:50:12 2011 -0500 better consensus; a little more robust commit 454da4754ac503edda5b1329b67757d797e46e07 Author: Heng Li Date: Fri Dec 2 00:20:22 2011 -0500 in pileup call remove_B() commit ff2bcac1cc078ba1879f18c89cfae314439d7086 Author: Heng Li Date: Fri Dec 2 00:17:32 2011 -0500 working on a few toy examples commit 745ca7260158d6df7897b52598033ffb055a9e4f Author: Heng Li Date: Thu Dec 1 22:55:39 2011 -0500 bam_remove_B(); not tested commit 07e4cdc7300abfcc82e03105b4689f95cab551cd Author: Heng Li Date: Thu Nov 10 12:58:55 2011 -0500 baseQ threshold on plain pipleup; removed -E commit 322ebf2082dfa91df44b3a996d26c85357e5d5a2 Author: Heng Li Date: Wed Oct 19 09:28:04 2011 -0400 fixed two gcc warnings commit a632457b4c4adc50d833b56b5a5231feafaf8193 Author: Heng Li Date: Tue Oct 4 10:13:23 2011 -0400 change size_t to uint32_t in bam_header_t This may cause issues on 64-bit big-endian machines. Reported and fixed by Paolo Emilio Mazzon. commit af31bf5a78aea03baf6eb90fe50076549d499f6e Author: Heng Li Date: Mon Sep 26 20:17:57 2011 -0400 rename pad2unpad to depad commit 77b198b73dfad1048e5d1c5a64aa75ee7b90f596 Author: Heng Li Date: Fri Sep 23 01:22:40 2011 -0400 convert padded BAM to unpadded BAM commit adb9e2342b7b7501d9527d3c23afab10469ae2c6 Author: Heng Li Date: Wed Sep 7 11:40:50 2011 -0400 generate template cigar with "fixmate" commit 46e5ab445a0fe880216cbc0daf1225725b569d7a Author: Heng Li Date: Fri Sep 2 12:50:18 2011 -0400 update kseq.h to the latest version commit 68e9e4a73eb91405bb3e56bf0cdaf12d1b487abb Author: Heng Li Date: Fri Sep 2 12:44:45 2011 -0400 Release samtools-0.1.18 commit aa06bdadb2d109a79f927f478102f96a1f5fd258 Author: Heng Li Date: Fri Sep 2 12:14:17 2011 -0400 updated the revision number commit 267e1e1b6e54c0ab24f94cd9aee9cbd2d1923f9f Merge: 19ff1d3 aebab30 Author: Heng Li Date: Fri Sep 2 12:13:08 2011 -0400 Merge https://github.com/lh3/samtools into reduce Conflicts: bam_md.c Fixed a few typos in the merge commit aebab302399c24eaa6c5ab79d13d6bd5e2e9ea9a Merge: c2c63d0 da62663 Author: Heng Li Date: Fri Sep 2 09:03:49 2011 -0700 Merge pull request #4 from peterjc/x_equals2 Implement basic support for =/X CIGAR operations commit 19ff1d3d7f47d7e61b121292aefe5a74bb8a18d2 Author: Heng Li Date: Thu Aug 25 16:38:12 2011 -0400 reduce BAM size (experimental) commit da626630fd98fd4e07ceb4d58c5c9a42d312a85d Author: peterjc Date: Mon Aug 22 06:58:08 2011 +0100 Support =/X CIGAR operations (treated like M) commit 461d8003529db77a4d5ecbd108312e868b051a3d Author: peterjc Date: Mon Aug 22 05:52:56 2011 +0100 Define CIGAR equals and X operationss (7 and 8) commit c2c63d067113baab41f3bc35fb28f4f00578accb Merge: 7ab3ef3 9a0ed9a Author: Heng Li Date: Thu Aug 18 17:21:54 2011 -0700 Merge pull request #3 from peterjc/x_equals Accept SAM files using = in CIGAR (treats X and = as M) commit 9a0ed9a6b85c7981465f459300208dbd93e3c6f5 Author: peterjc Date: Thu Aug 18 19:28:52 2011 +0100 Accept SAM files using = in CIGAR (treats X and = as M) commit 7ab3ef388c1eb34d7912fd70cc5656c955240263 Author: Heng Li Date: Mon Aug 8 10:22:22 2011 -0400 bugfix: indexing takes huge memory This happens when an unmapped mate has coordinate 1. Thank Joel Martin for the fix. commit a3f6738593e944354a8f75306687d8b3acf08bf1 Merge: a8bdca9 bc67ea2 Author: Heng Li Date: Mon Aug 8 09:52:26 2011 -0400 Merge branch 'master' of github.com:lh3/samtools commit bc67ea225da653f36a70b38382d6111dd494f659 Author: Petr Danecek Date: Thu Jul 28 20:03:16 2011 +0100 Variant Distance Bias commit deb578f0c49d0b7d8c3bc6be220b4d67e2e7dfdf Author: Petr Danecek Date: Tue Jul 26 09:57:37 2011 +0100 If there is only one RG tag present in the header and reads are not annotated, don't refuse to work but use the tag instead. commit a8bdca9cf482a637b89ee4f98469a93e0ab5e69b Author: Heng Li Date: Mon Jul 25 10:10:55 2011 -0400 bugfix: LRT2=nan commit 0afe33137d046a3e849eeb4a54590f27cbad4228 Author: Heng Li Date: Fri Jul 22 21:55:38 2011 -0400 fixed a bug/typo commit 62d5849658c10222d40308c6b53ab4f99a448494 Author: Heng Li Date: Fri Jul 15 16:04:19 2011 -0400 allow to set see in subsampling commit 5f46243824cc9435b167973e1d51e13128794ea1 Author: Heng Li Date: Fri Jul 15 15:54:47 2011 -0400 support subsampling commit 5e55b6f34fc86cba7cf98d52ccaed405c3ffabbc Author: Heng Li Date: Fri Jul 15 15:53:38 2011 -0400 support indels commit f31c162926d6f43e8b60171789a258d02e1f9be5 Author: Heng Li Date: Thu Jul 7 17:02:33 2011 -0400 do not count indel with "view -Y" commit e412dae587883b4c17e5fbf4b7c33f38bfa8458a Author: Heng Li Date: Thu Jul 7 00:35:25 2011 -0400 for WIN32 compatibility commit 70a52501bcfa63824749893a5ab8ed3c38e34958 Author: Heng Li Date: Thu Jul 7 00:32:46 2011 -0400 for WIN32 compatibility commit 00438f14ed5984f08e8f7645a9b95644a812f969 Author: Heng Li Date: Wed Jul 6 23:41:45 2011 -0400 fixed an uninitialized variable commit 7609c4a01059c326544b3d0142dfe9c4229d68c6 Author: Heng Li Date: Wed Jul 6 23:39:31 2011 -0400 fixed an uninitialized variable commit cec7189a412f80ccb068a73bd28528915c16b0bf Author: Heng Li Date: Wed Jul 6 22:53:19 2011 -0400 Release samtools-0.1.17 commit 93c06a249de3bb666029bf07b66de5e8e5e314fa Author: Heng Li Date: Wed Jul 6 09:46:09 2011 -0400 bugfix: incorrect idxstats for the last seq Again, this bug is caused by 3rd-party code for the sorting order checking. commit 84f6ca62db6e27b8c4c711e7b5f3ca704bf27b4f Author: Heng Li Date: Tue Jul 5 23:30:23 2011 -0400 output mapping quality in the old pileup format commit 362e05fd670886acaede69b864903d730b9db3ca Author: Heng Li Date: Tue Jul 5 21:59:22 2011 -0400 added a brief description of the VCF format commit e690a696468205e0cc4560016361c997660dd496 Author: Heng Li Date: Tue Jul 5 16:23:10 2011 -0400 improved samtools manual page commit 362b4a1408ef3c32311d638aa8d85ce39c1c7b2d Author: Heng Li Date: Tue Jul 5 15:58:29 2011 -0400 merge bcftools.1 to samtools.1 commit 643e0e61ba7266efbc9e5bfcb8e41f369ba2ce0a Author: Heng Li Date: Tue Jul 5 13:39:02 2011 -0400 mpileup: when region set, set reference properly commit 613e4d67624a94f62563935fbd5cc294df69605a Author: Heng Li Date: Mon Jul 4 23:29:02 2011 -0400 compute the min PL diff commit 5b7d5d3f52b97ca42c8500eede808dab88a46a53 Author: Heng Li Date: Mon Jul 4 22:57:48 2011 -0400 rename trio.c to mut.c commit 84fe96ad64b0365ead93a4115d1684b9bebb98fc Author: Heng Li Date: Sun Jul 3 15:38:51 2011 -0400 added pair caller interface; not tested commit 2f2867b87b84c35319cc416d6173819d5c8a4e8c Author: Heng Li Date: Sun Jul 3 15:24:23 2011 -0400 inital implementation of a pair caller commit e97653cf2ad653c95886933c42a2b5492ccab5ff Author: Heng Li Date: Sun Jul 3 00:06:28 2011 -0400 convert bam to single-end fastq commit e8013e11f7a8db0a8d18c60d130169cca39bf2bd Author: Heng Li Date: Sat Jul 2 14:39:18 2011 -0400 improve BED parsing commit 1025714325fdc636aeee47a76db8dafbbbfde64b Author: Heng Li Date: Fri Jul 1 14:19:54 2011 -0400 update the manual page commit 8022d0039dff47b1c11b2421357d510c1f28ae15 Author: Heng Li Date: Fri Jul 1 14:17:03 2011 -0400 output the best constrained genotypes in trio commit 18c87295e12f5bebafdcae00d52000fb94c8a566 Author: Heng Li Date: Fri Jul 1 11:18:14 2011 -0400 added documentations for view -T commit daf7a8d96bd495296bf7c7d99cddb808a3ced7d5 Author: Heng Li Date: Thu Jun 30 22:45:20 2011 -0400 fixed a bug in writing SP commit e5c32bf9b28c6e3e861db88de56b5dbe11058b61 Author: Heng Li Date: Thu Jun 30 22:35:25 2011 -0400 optionally output read positions in mpileup commit 1008051155ec994c1901e18f3eb03ea32a62e5d7 Author: Heng Li Date: Thu Jun 30 22:17:25 2011 -0400 make faidx works with <2GB lines commit 2daebb63762425dd3074ddf71582ad189001e394 Author: Heng Li Date: Thu Jun 30 17:28:58 2011 -0400 fixed an issue in the trio caller and the indel caller commit 9fdd52cf0716fb342a94946433d564b28b230835 Author: Heng Li Date: Thu Jun 30 13:34:01 2011 -0400 Added trio caller; NOT tested yet commit ea22a8ed83625e9c82382b56acc42a2d9cfd17e5 Author: Heng Li Date: Thu Jun 30 11:42:29 2011 -0400 convert PL to 10-likelihood GL commit 10d7065267b0d12c2bfcb6c70204fb6944cd395d Author: Heng Li Date: Thu Jun 30 10:49:05 2011 -0400 fix a compatibility issue with the new bcftools commit d340f01f609c61b719d38a6a55629a3fc899e1cd Author: Heng Li Date: Sun Jun 26 23:41:20 2011 -0400 allow to ignore RG commit d6321faf98ebfe899b9409fb23c90a4aa8c6b542 Author: Heng Li Date: Sun Jun 5 23:05:21 2011 -0400 fixed a bug in SO checking due to a recent change commit bc995abf666d0c9ab4258f6c1b3518a45a89209f Author: Heng Li Date: Fri Jun 3 14:45:36 2011 -0400 update the version number commit 9e7cd83a08383858d008e0ccb2238a2b93831d6c Author: Heng Li Date: Fri Jun 3 14:43:12 2011 -0400 smarter way to parse a region string commit e58a90a0fde54053dac65352b34c13c3fea815fc Author: Heng Li Date: Wed Jun 1 14:36:22 2011 -0400 output LRT2 instead of LRT1 commit 08f78c9af3e5661f04f80bef424232de721dba03 Author: Heng Li Date: Wed Jun 1 14:02:28 2011 -0400 genotype test, but assuming 1-degree commit 587b852340d7e60f6f7cf474a92ef77aeab46018 Author: Heng Li Date: Wed Jun 1 12:55:19 2011 -0400 perform 2-degree test by default commit 3d38e403c5c830478b7eb157a484776997440501 Author: Heng Li Date: Wed Jun 1 12:44:34 2011 -0400 fixed a typo; but the result is still not good commit 06291624f7dcc57445676f3be25d0bc355dd7110 Author: Heng Li Date: Wed Jun 1 12:24:18 2011 -0400 fixed a typo commit 63b98aa33636b0d82a435bf49153c8c1502e7d42 Author: Heng Li Date: Wed Jun 1 12:23:37 2011 -0400 added HWE+F<0 filter commit 37d926e8999999b593d0637ab7dc379dbd3d6006 Author: Heng Li Date: Wed May 4 10:11:59 2011 -0400 improved sorting order checking in index Patches from Jonathan Manning commit 1c2dc6762c5f7cd946046b53346513f2f9761dbf Author: Heng Li Date: Tue May 3 23:09:05 2011 -0400 added r^2 estimate; added Brent's method commit c2d3bcd8f98e31668b5f1321222fbc6fd6336e75 Author: Heng Li Date: Sun May 1 23:45:23 2011 -0400 combine several utilites into vcfutils.lua commit be2e7362d7593ea4d03fb33cdb6af2aa096ca6c4 Author: Heng Li Date: Wed Apr 27 21:09:22 2011 -0400 minor warning commit 683ef0443860813d743cf84fa86dda9bfaf5445a Author: Heng Li Date: Wed Apr 27 10:10:38 2011 -0400 added versioning commit ed72f25ec85671f7646dbc92fa7b5b1dda427f7d Author: Heng Li Date: Wed Apr 27 10:04:02 2011 -0400 Output ML allele count commit 2a9e36d2d6c405b2411ca47458f028ada8fe1000 Author: Heng Li Date: Tue Apr 26 16:14:20 2011 -0400 use ar -s commit 7a4f54e6dbcd7c94acbb3f1050a93f94b8a07949 Author: Heng Li Date: Sat Apr 23 01:22:31 2011 -0400 added another type of LRT commit b9c5e84762a4aacce3a3771b51ea80967c79a2e5 Author: Heng Li Date: Fri Apr 22 16:00:31 2011 -0400 added version commit 8fad6677c5952efd67391581d64e67e02e7f6e68 Author: Heng Li Date: Fri Apr 22 00:30:19 2011 -0400 remove the pileup command commit 3a962fb6ebf779de70f9e6effb2d8701a9aa3dd9 Author: Heng Li Date: Thu Apr 21 23:10:45 2011 -0400 Release 0.1.16 (r963:234) commit b4d683cffbd98c43f05aff8610b37d63dd7e54aa Author: Heng Li Date: Thu Apr 21 12:44:44 2011 -0400 fixed a bug when coordinate-less reads are on the reverse strand commit c5ec45a128f409debc6a56a798024f53004037dc Author: Heng Li Date: Wed Apr 20 11:36:52 2011 -0400 added option '-f' to merge to avoid overwritting commit 68d431531370d24907c01a27f166f2341d7c4d35 Author: Heng Li Date: Wed Apr 20 10:26:58 2011 -0400 do not print a warning commit 32922607e51ad2260c337eb022b9e4aedacb049f Author: Heng Li Date: Wed Apr 20 10:21:06 2011 -0400 Added ldpair to compute LD between requested pairs commit b8d6fa71b91678fa02338257e0707d1e5ca098dd Author: Heng Li Date: Sun Apr 17 21:51:43 2011 -0400 On a toy sample, type "B" seems to be accepted commit 0e7ee9a6bb4029184202aa6e6738105ba0c0510b Author: Heng Li Date: Sun Apr 17 21:21:20 2011 -0400 added type "B"; not tested yet commit a513dfad0ac0062b03871eb6ecf26cb8d18dc895 Author: Heng Li Date: Sun Apr 17 19:25:54 2011 -0400 fixed a bug in bedidx.c: input BED not sorted commit de1e192bb0a8a762a54a6eee81d882fab01c3d32 Author: Heng Li Date: Sun Apr 17 18:51:08 2011 -0400 by default, always perform posterior chi^2 commit df6e0d1099895fc6cd7a19dc89fba95ed6654d35 Author: Heng Li Date: Sat Apr 16 12:33:28 2011 -0400 added debugging commit 8ce52e024dc2ef361dbd5399c232163055057e70 Author: Heng Li Date: Sat Apr 16 00:59:05 2011 -0400 avoid a segfault given wrong input commit e66b6684fc9a397f91ec29fdeecae9f8eb986a55 Author: Heng Li Date: Fri Apr 15 19:55:39 2011 -0400 do not segfault when there is no PL commit 9ce3c584ec0cebfa45576f2ef538df4dad2b7e55 Author: Heng Li Date: Fri Apr 15 11:59:55 2011 -0400 remove another unused part commit f53a051d68bf312ac8d5865210fae7a9808c0fb9 Author: Heng Li Date: Fri Apr 15 10:41:25 2011 -0400 print G3 if HWE is small commit 4b2c08bb86ca4ed4959e4cb77a28f7d6fc19f5c9 Author: Heng Li Date: Fri Apr 15 10:04:34 2011 -0400 fixed a bug actually not fix, but hide it commit 088e13c32453fb533b7bb1c65a573f9b90a23625 Author: Heng Li Date: Fri Apr 15 09:48:47 2011 -0400 added LRT based permutation; not used though commit 1e3c2001afcb80b5eaa4c3f88df9da7b01b62524 Author: Heng Li Date: Fri Apr 15 09:28:55 2011 -0400 Perform posterior contrast for small LRT Posterior contrast is much slower than LRT. Nonetheless, posterior P-value is more robust to sequencing artifacts. Thus we may combine the two to achieve a balance between speed and low FPR. commit 6f1b066270902198a7175ff6c1b05ebc8d1919be Author: Heng Li Date: Fri Apr 15 01:36:06 2011 -0400 Added Brent's method commit 3d061e5db25b67b25f6ff87afe4162e121354232 Author: Heng Li Date: Thu Apr 14 23:30:10 2011 -0400 fixed a typo in printing commit 7fd14ceb5990bb350b8e97346ef3537d80058def Author: Heng Li Date: Thu Apr 14 23:14:23 2011 -0400 fixed a stupid bug commit f5b2c3459ec098b3cafd9619b9077132516baf58 Author: Heng Li Date: Thu Apr 14 22:42:35 2011 -0400 separate EM and posterior Now, constrast is not performed unless -C is in use. EM can be invoked independently with -e without computing the posterior. commit 9eefcac963697fae554789b11ae3cb2c23f224d0 Author: Heng Li Date: Thu Apr 14 22:00:19 2011 -0400 further code cleanup; prepare to add EM interface commit c2cce52355262743711e4742b0c8542bfcab1cdd Author: Heng Li Date: Thu Apr 14 21:44:03 2011 -0400 drop EM from prob1 commit 24016f04bd3bdffb7eeb50cb25854f5007feb70f Author: Heng Li Date: Thu Apr 14 21:08:33 2011 -0400 drop posterior LRT; prepare for clean up commit 3670d8bd88c3eb22873f0a80e2a5913f64ca8c9a Author: Heng Li Date: Thu Apr 14 20:57:43 2011 -0400 better initial values for LD commit d48a8873c060b18b57799cfe3a0e5496ba069457 Author: Heng Li Date: Thu Apr 14 20:36:25 2011 -0400 finished EM commit b101f2db476188a950c23f5c1b6185fdb7f8f40b Author: Heng Li Date: Wed Apr 13 01:19:04 2011 -0400 genotype frequency estimate commit d79bdcbf6242ecfb8accba9ac9a22fbcbd543cf2 Author: Heng Li Date: Wed Apr 13 00:37:22 2011 -0400 prepare for code clean up commit e0ce416abfc094f0c090957080b1404fd0edf752 Author: Heng Li Date: Wed Apr 13 00:34:15 2011 -0400 rename ld.c to em.c commit 45ede3ad181f35c1be24bed5d75841e472357ab7 Author: Heng Li Date: Wed Apr 13 00:22:10 2011 -0400 implemeted EM likelihood ratio test The idea is learned from a brief chat with Rasmus Nielsen. commit 0454a346b60e42b75a2f742272089810279c7131 Author: Heng Li Date: Tue Apr 12 15:45:52 2011 -0400 added likelihood-ratio test (idea from Nick) commit f6287c8646c690440a1554c8958e7268f4134dc2 Author: Heng Li Date: Sun Apr 10 18:24:37 2011 -0400 Release samtools-0.1.15 (r949:203) commit de6023f38f4d652438557cf7a0ac6eec324e7416 Author: Heng Li Date: Sun Apr 10 15:54:58 2011 -0400 improved help information commit d3b337f2b7eda1e6f8f5575a19d1b5ed55cae279 Author: Heng Li Date: Sat Apr 9 16:28:01 2011 -0400 fixed a minor issue commit 82f6e4f49247e75fbd8ec08c285b8d3047b3d235 Author: Heng Li Date: Sat Apr 9 15:49:04 2011 -0400 separate QC-pass and QC-fail reads commit 8362b4a255081ee7ca0a4ca2eabc8c76758b6863 Author: Heng Li Date: Fri Apr 8 17:45:19 2011 -0400 added verbose level commit f7bf419c290462be7d289249a4a6d28f825b4c93 Author: Heng Li Date: Fri Apr 8 16:08:14 2011 -0400 fixed a bug commit 890cbb1ac93b3004fb6cf42ff47195077dcfc8ad Author: Heng Li Date: Fri Apr 8 16:00:37 2011 -0400 drop unrelated @RG when "-R" is in use commit a62dc929c950fb51311b705f5b5bfba8e3f704d7 Author: Heng Li Date: Fri Apr 8 16:00:14 2011 -0400 skip header validation commit 39da810e2c56c8f0eff1ab726600b41f26d3d8e9 Author: Heng Li Date: Tue Apr 5 23:52:22 2011 -0400 change error message commit c0c50a34df250ef8a7a29b172058cd229be582b5 Author: Heng Li Date: Tue Apr 5 23:50:46 2011 -0400 fixed a bug caused by recent modifications commit 25226e8c468404cb5e1b5272efcea57e4193c762 Author: Heng Li Date: Tue Apr 5 13:31:19 2011 -0400 reduce the indel filtering window commit 5e18d7014437734f9dac9ab45a95e43ec2526101 Author: Heng Li Date: Mon Apr 4 13:56:20 2011 -0400 only output hwe if it is small enough commit 614941fb7dd276de662e7820eb8c7bae871a18cc Author: Heng Li Date: Mon Apr 4 13:34:02 2011 -0400 added HWE back commit 7abe8825aa0bacccdeb38125934ae94d18f0ad4d Author: Heng Li Date: Mon Apr 4 12:46:24 2011 -0400 EM estimate of genotype frequency commit 2bfeff9c645d177416664f1cb811e85cac3ff9e3 Author: Heng Li Date: Mon Apr 4 11:29:12 2011 -0400 minor commit 401e40647e7e3abbac6e4ec3d8bb68eb6f2d401b Author: Heng Li Date: Mon Apr 4 11:24:04 2011 -0400 Added genotype freq estimate and association test commit 6cc226df6e3b480f1bd6e763ce8ef47f785bbb74 Author: Heng Li Date: Sun Apr 3 20:57:23 2011 -0400 minor changes commit 7e47a39630e812f09b80369f14606245976f687e Author: Heng Li Date: Fri Apr 1 15:21:59 2011 -0400 print the grayscale commit 2f675d9c0dde3c166c99e335fa17c7873a5ae8d5 Author: Heng Li Date: Fri Apr 1 08:55:16 2011 -0400 change to comment commit 0592bb514994544ed84f51e509b233cf8821e0cf Author: Heng Li Date: Fri Apr 1 08:54:35 2011 -0400 added base quality filtering commit fc1b47e04a7b94f6362c45856cbeb89d9d0b5ca5 Author: Heng Li Date: Thu Mar 31 23:31:14 2011 -0400 fixed a few typos in comments commit 60be79bc8f0d24656e5e8a329af7e9b5b91d4c8b Author: Heng Li Date: Thu Mar 31 23:13:23 2011 -0400 comments commit 2432864acc25ebe5cee4217dbb0120439077a7f8 Author: Heng Li Date: Thu Mar 31 22:42:46 2011 -0400 added bam2depth.c, a demo program commit 39625f7c6bea9ccbfd9af0feb22348d52079f012 Author: Heng Li Date: Thu Mar 31 16:37:22 2011 -0400 added bgzf_check_bgzf() (used by tabix) commit 6de6bd3fb67fd22753a5f07d4cc25bf94e1b5a8c Author: Heng Li Date: Thu Mar 31 16:37:08 2011 -0400 fixed a bug in bedidx.c commit 3b9e257d25b2e81eed1625bc5d2882ed486ef20e Author: Heng Li Date: Wed Mar 30 13:27:15 2011 -0400 added bed support to bcftools commit 47bcce3d14ec4d205283b61e5e653803996c42e0 Author: Heng Li Date: Wed Mar 30 12:56:40 2011 -0400 Added BED support to "samtools view" commit a812386017faedfc86c0e6562adbb2138329cfeb Author: Heng Li Date: Wed Mar 30 12:47:04 2011 -0400 support BED file commit 3052dddc929f1825e6e7f7f6f6724d9465d6cf9a Author: Heng Li Date: Mon Mar 28 15:51:55 2011 -0400 relax RG matching; proper mismatching message commit f86d60c8fe25785523f01fae1486d2a6df4ee6ef Author: Heng Li Date: Sat Mar 26 10:38:23 2011 -0400 Avoid reporting association when something unexpected, which I do not understand, happens. commit dd41e6b26fd9fe30218748b9a0a1f49bdb1862b9 Author: Heng Li Date: Sat Mar 26 10:38:01 2011 -0400 Added -1 to merge commit 4a0364b0d7f87f1c88d71ec5857a1f1d40710681 Author: Heng Li Date: Wed Mar 23 16:56:55 2011 -0400 plot pairwise r^2 commit 452629a711582e612bec22b3b082e234bd37039b Author: Heng Li Date: Wed Mar 23 14:31:01 2011 -0400 pairwise LD; case-control AF2 commit 52862951adcaecde26ba8f0d9c1897944640a674 Author: Heng Li Date: Mon Mar 21 23:03:14 2011 -0400 Release samtools-0.1.14 (r933:170) commit 59a5a8ba8e2940f0e38238f9339f02c91a8a0ce4 Author: Heng Li Date: Mon Mar 21 13:52:55 2011 -0400 optionally skip loci with too low sample coverage commit 6434264b5c69514d4fafe62cbd30b3bbaddc1d41 Author: Heng Li Date: Sat Mar 19 14:38:25 2011 -0400 mpileup support Illumina1.3+ quality; skip non-variant sites when "view -v" is in use commit 5f59e01987e1d5eca7d6359cae64a9734b18beea Author: Heng Li Date: Fri Mar 18 17:19:18 2011 -0400 update version to r933:167 commit 4d2c3c950910aa3d2c87760c3532e458fe01c0fa Author: Heng Li Date: Fri Mar 18 16:25:01 2011 -0400 added "-1" to the command-line help commit 55313a015a7bd6369cf5a66fed7fab2333201dc9 Author: Heng Li Date: Fri Mar 18 16:22:12 2011 -0400 added the "cat" command (by Chris Saunders) commit b670272cadf3efa4dc456ac4c76104f73477d60d Author: Heng Li Date: Fri Mar 18 15:59:46 2011 -0400 support varying the compression level commit c5dd3c9ca5f75f880e52c8cd2beae983bcb8d3b1 Author: Heng Li Date: Wed Mar 16 14:33:45 2011 -0400 update the manual pages commit 12fb4b596dc51bccd154fc4bd0593442f7937a46 Author: Heng Li Date: Wed Mar 16 12:49:26 2011 -0400 update changelog commit e7fe4fd66e02d60a1ca7952ad1938809e77729a9 Author: Heng Li Date: Wed Mar 16 12:10:05 2011 -0400 do not call indels when the depth is very high commit 7455eeaa32b949bb3856f75810890aabf7cacb18 Author: Heng Li Date: Wed Mar 16 11:56:56 2011 -0400 code clean up commit 5f16679e54ced8e67a75d949f9175c50480b914e Author: Heng Li Date: Tue Mar 15 14:45:24 2011 -0400 when -s is specified, change the sample order commit 7ba95adee09d3b06a7eaf797d25efef837e592f5 Author: Heng Li Date: Tue Mar 15 14:11:42 2011 -0400 compute the rank in permutation commit d219783cea7643fc7e10e1bd3a98e9b3165b4506 Author: Heng Li Date: Sun Mar 13 21:35:13 2011 -0400 I have found a SERIOUS BUG!!! commit 8e20d04ecdac1a7788eef71c4bb91b8479cf7150 Author: Heng Li Date: Sun Mar 13 17:04:04 2011 -0400 optionally shuffle samples in a BCF (debugging) commit fc7b261f181f2a411427bc9ee5d586c883ca9cdc Author: Heng Li Date: Fri Mar 11 09:34:20 2011 -0500 fixed a bug commit b3bbcc3d40994ae85705ab6fef9866ec8c142201 Author: Heng Li Date: Thu Mar 10 20:25:59 2011 -0500 use mode instead of mean commit f1161262d137098a19143b5cb0de810e5db3243e Author: Heng Li Date: Thu Mar 10 20:09:16 2011 -0500 start from the mean instead of the mode commit 2ba56f5e99e90674855c4ffc8bf583340b932e1e Author: Heng Li Date: Thu Mar 10 17:13:34 2011 -0500 fixed an error in Chi^2 test commit b4ce7ae400290bc43dd287240479667f99b3b11e Author: Heng Li Date: Thu Mar 10 00:23:39 2011 -0500 minor commit 8487fa5d3a73a43443964e731ea2a4c873c9d4e5 Author: Heng Li Date: Wed Mar 9 21:33:19 2011 -0500 added -F to accept BCFs generated by old samtools commit fd51d2093f7fd775a7eaaeea57fa34716ab59ac2 Author: Heng Li Date: Wed Mar 9 17:39:09 2011 -0500 update version commit b6da54335df943015a998a934075331b467abb5b Author: Heng Li Date: Wed Mar 9 17:37:14 2011 -0500 compute pseudo-chi2 probability commit 9f73cefdb8935421d872b989dd98fbc8e1295029 Author: Heng Li Date: Wed Mar 9 15:54:04 2011 -0500 remove a comment which is wrong commit b10b1e47ece522e97ab8ef23417bcb6454f8b9db Author: Heng Li Date: Wed Mar 9 15:51:12 2011 -0500 clean up commit 353bfae2c6ff59205bd9223db04084cf7f507f01 Author: Heng Li Date: Wed Mar 9 15:45:29 2011 -0500 for backup commit 53915d1c6410c2537d18bfa8eb8c657a2233c35e Author: Heng Li Date: Wed Mar 9 15:27:56 2011 -0500 having debugging code commit 0d0dbf66995b1511390d593981eae7b5d36fe17b Author: Heng Li Date: Wed Mar 9 14:58:23 2011 -0500 temporary backup commit 5b74a174a8b637dee43b7f30250df6fb96580e12 Author: Heng Li Date: Tue Mar 8 15:46:11 2011 -0500 the output makes sense, but there may be a typo... commit d81ec654b6c0c1eef6b0625d96f14b3155cee7c6 Author: Heng Li Date: Tue Mar 8 15:19:09 2011 -0500 added contrast2(); fixed a bug in haploid mode commit 0cfd896fad5f7737cca49efa94a11892dafcd812 Author: Heng Li Date: Mon Mar 7 21:40:17 2011 -0500 fixed a bug in haploid genotyping commit ccd52155ef61273f2b42ad9c7b31ff1915f81b24 Author: Heng Li Date: Sat Mar 5 18:10:35 2011 -0500 fixed a few bugs; still not fully working commit edc3af753f96f831968ae32f2e0f915b74f31e6e Author: Heng Li Date: Fri Mar 4 17:31:33 2011 -0500 drop HWE calculation commit 92dac194debb66ca0718c21c871822dda2dd5bc1 Author: Heng Li Date: Fri Mar 4 17:28:35 2011 -0500 implemented hap/dipoind mode; probably BUGGY! commit 7f26804bc27937e36fdc967e5c76514653ea40f5 Author: Heng Li Date: Fri Mar 4 16:01:27 2011 -0500 read ploidy commit e7b7213475b5e61a69aab77ffb02b4983c8e7678 Author: Heng Li Date: Fri Mar 4 14:12:14 2011 -0500 added math notes commit 46023e2f21321da83fc8e83e9229757a4e821acb Author: Heng Li Date: Fri Mar 4 13:34:10 2011 -0500 update BCF spec commit 13190c49eeb006ad7013b7f1e9fc1b3beca3ae78 Author: Heng Li Date: Tue Mar 1 14:45:19 2011 -0500 Release samtools-0.1.13 (r926:134) commit be8fabbb6001d9fd5263a70a3e21ed6dfe5a9837 Author: Heng Li Date: Tue Mar 1 14:07:15 2011 -0500 prepare to finalize 0.1.13 commit 1e8c753660978bed7e9289fe50becd596d9314bb Author: Heng Li Date: Tue Mar 1 09:40:17 2011 -0500 allow to change whether to drop ambiguous reads commit 412210bfdb46606023f2e4b9086f2787f0cf1c62 Author: Heng Li Date: Mon Feb 28 22:01:29 2011 -0500 revert to the old behavior of phase commit 46035589518cf84738de8666b866e2619457c1fb Author: Heng Li Date: Mon Feb 28 16:46:23 2011 -0500 change version number commit 7f40c33e37fc16fcb0a375ce46ae1d09cafb6d50 Author: Heng Li Date: Mon Feb 28 16:37:42 2011 -0500 bugfix in indel calling: interger overflow commit 75849470efbe30042e5ddd516f9bcbe3b9bf6062 Author: Heng Li Date: Mon Feb 28 15:35:47 2011 -0500 fixed a typo commit 9e6fb569885f906fabaab7fc2f02eae82f4bd602 Author: Heng Li Date: Mon Feb 28 15:34:09 2011 -0500 minor changes to heuristic rules commit 30a799a91f5e2c10b761aa5437f902c6649fceb3 Author: Heng Li Date: Mon Feb 28 15:20:26 2011 -0500 fixed a bug in the latest change commit e21ba9df950ea37f5c1b35c2af9ba9a4e0bba02a Author: Heng Li Date: Mon Feb 28 12:47:06 2011 -0500 put version in bam.h commit 918b14780c1dceb39c7010638ecd61c626e17166 Author: Heng Li Date: Mon Feb 28 12:00:38 2011 -0500 frag_t::phased==0 reads are dumped to chimera.bam commit 657293c7bdba3ac69f53cd1ffa2874ed8756475e Author: Heng Li Date: Mon Feb 28 11:05:29 2011 -0500 change default -q to 37 (previously 40) commit 33d8d3bea76e466798ea322d68d34deb8d2dff06 Author: Heng Li Date: Mon Feb 28 10:39:57 2011 -0500 fixed a minor bug in BAM reading commit daa25d426d42465d76c7317c95772bbb36bb3f47 Author: Heng Li Date: Sat Feb 26 21:07:24 2011 -0500 suppress gzopen64() warning commit 9cec4256eb9e7848d4711adb67b540659c141e32 Author: Heng Li Date: Fri Feb 25 22:14:52 2011 -0500 fixed a long existing bug in vcf2fq commit 304487c83067a733add71cbc3886fa8c49f7ef2a Author: Heng Li Date: Fri Feb 25 16:37:40 2011 -0500 change version number commit 10ba6bf4f16692760f696f7b17f3719065786f77 Author: Heng Li Date: Fri Feb 25 16:34:08 2011 -0500 Change the order of PL; change SP to int32_t commit c5cc2a8036a9c3579fbfde651efec4f6763b0228 Author: Heng Li Date: Fri Feb 25 14:52:03 2011 -0500 claim X defined in the header commit 4ee8cb29f6092fd14a89f0cc5d3575112a204f39 Author: Heng Li Date: Fri Feb 25 14:40:24 2011 -0500 minor changes commit 00065e9336a2831dc53bee7da2f4719845be1a2a Author: Heng Li Date: Fri Feb 25 11:39:06 2011 -0500 fixed an error in the BCF spec commit 1e2a73afcb72a02aa448718cb017c0438de89f90 Author: Heng Li Date: Fri Feb 25 11:36:40 2011 -0500 update BCF spec commit dbf8eedaa38a405cb2fba5b3952b85776f51d035 Author: Heng Li Date: Fri Feb 25 11:28:43 2011 -0500 update BCF spec commit eed1d91af9fad3c9d965333a55e623757f9c4e9d Author: Heng Li Date: Fri Feb 25 09:51:39 2011 -0500 fixed a flaw in targetcut commit 59bc980bb832b92a8b0cc244cf106e6150e4db6f Author: Heng Li Date: Fri Feb 25 00:54:35 2011 -0500 update manual page commit fcc4738c4abdca79e3de159e21208df1b98ac76c Author: Heng Li Date: Fri Feb 25 00:45:39 2011 -0500 update version format commit 5748639ae542b7f6b853562edc2bb3faf43030e4 Author: Heng Li Date: Fri Feb 25 00:45:12 2011 -0500 update version number commit 06b44cc366cf27ce8976ee6a05810a0b3c48b56d Author: Heng Li Date: Fri Feb 25 00:44:21 2011 -0500 update version number commit ab7f4529d12739ff66fd4c09af9d992ab59c53ef Author: Heng Li Date: Fri Feb 25 00:42:55 2011 -0500 various help message commit a092e1f6f963272f8bb23616986ddaf604fd0f82 Author: Heng Li Date: Thu Feb 24 23:43:13 2011 -0500 disable unfinished functionality commit f00a78db72b14ee4c6689fc13f20ed31aeaecd40 Author: Heng Li Date: Thu Feb 24 10:04:56 2011 -0500 added "const" to bcf_p1_cal() commit 91049c4a8db3bf50dcc9d07506f22fa4ca5b5a96 Author: Heng Li Date: Wed Feb 23 11:53:47 2011 -0500 randomly allocate unphased reads commit f4405354a8d4cb3441141fa734573031059d7f57 Author: Heng Li Date: Tue Feb 22 15:36:07 2011 -0500 fixed a typo commit 3075e4dc5c7c9d954426aabda6a73fa788357100 Author: Heng Li Date: Tue Feb 22 15:33:40 2011 -0500 make output more informative commit 628cf3235e2815a40acf089fb1d3357be6437787 Author: Heng Li Date: Tue Feb 22 14:50:06 2011 -0500 change the scoring rule; change default k to 13 commit f22fd99831e4b5c74f898719216f359dbe987bbf Author: Heng Li Date: Tue Feb 22 14:45:15 2011 -0500 update scoring in masking commit 2f23547b81984555032aa0eefd064b8e07986fdc Author: Heng Li Date: Tue Feb 22 14:37:17 2011 -0500 remove dropreg() commit 4d8b6b1f1f331ca9041983c66e34a857c3b8f1bb Author: Heng Li Date: Tue Feb 22 13:10:16 2011 -0500 accept files from stdin commit 9b50c5038e6fc0185e29ca5b50fe0806a9a939b9 Author: Heng Li Date: Tue Feb 22 11:16:57 2011 -0500 fixed a bug in consensus generation commit 1332ab32fb788fdc81b2ba8653b905d106238fad Author: Heng Li Date: Mon Feb 21 22:53:23 2011 -0500 print dropped fragments commit a288761b4ca1584e51076a71cbc4d72fe923dda1 Author: Heng Li Date: Mon Feb 21 22:37:04 2011 -0500 bugfix: singletons are not phased commit 683365f534c0223dea7d72532015ac16a45ba22b Author: Heng Li Date: Mon Feb 21 17:27:10 2011 -0500 output singleton blocks commit 841a4609084d81f1bc81e0b00dd806002461e7d9 Author: Heng Li Date: Mon Feb 21 15:58:55 2011 -0500 fixed a bug; not working with -l right now commit fdd57ea31732b5516dc212d72174b60206952636 Author: Heng Li Date: Mon Feb 21 15:17:00 2011 -0500 skip mapQ==0 reads commit 4eb6ba75c23c1c9be5f76814fa1b93a2e304b2af Author: Heng Li Date: Mon Feb 21 14:03:03 2011 -0500 print the "targetcut" command commit 0123d9559ba58b026c0dfd15bc26019a193cd21a Author: Heng Li Date: Mon Feb 21 11:22:13 2011 -0500 allow to set the maximum depth commit 0f92eb248a4d06645b2c3d736a0faea8a7a9f731 Author: Heng Li Date: Mon Feb 21 09:56:41 2011 -0500 use a proper error model to call hets commit 587a01504af5aea6288740d121dccf48fb8a75f4 Author: Heng Li Date: Mon Feb 21 09:16:38 2011 -0500 phase is UNFINISHED; strip RG when merging commit 723bf3cd79e4f4a558373d4c707fa6b3db0fb357 Author: Heng Li Date: Sat Feb 19 23:38:11 2011 -0500 use a proper model to compute consensus commit 891a6b02d4a9af2ed98fbaac4915bf1f0da4f6c8 Author: Heng Li Date: Sat Feb 19 22:14:19 2011 -0500 added comment commit 8b55e0a581ecc9e4ba754d1f3c8784f3038b6e48 Author: Heng Li Date: Fri Feb 18 17:23:39 2011 -0500 change the output format commit 75c36e8c563eddd0a362ba3b38cf0aea21aafb1f Author: Heng Li Date: Tue Feb 15 20:31:00 2011 -0500 fixed a bug in writing BAM commit bb0ce52f066cfebaa35a125d57b353bb717a5165 Author: Heng Li Date: Mon Feb 14 23:39:09 2011 -0500 skip uncovered; unknown alleles taken as X commit ba67f4d119c7d06907db3015d337d9a01a3fc9fe Author: Heng Li Date: Mon Feb 14 23:21:19 2011 -0500 fixed a bug commit e4448d49e6129a5e1ee9c7f04f43612f12d6aad6 Author: Heng Li Date: Mon Feb 14 22:43:09 2011 -0500 prepare to read hets from a list; unfinished commit 129ea29c1f12177c0a7c3e21676f6210370fc59b Author: Heng Li Date: Mon Feb 14 16:32:22 2011 -0500 updated khash.h to 0.2.5 commit 15b44ed93bd949dffcf79ac8dbea6d9b7dfcb58c Author: Heng Li Date: Mon Feb 14 16:15:04 2011 -0500 use the latest version of khash commit 486c05f06f44d981dfb2069bcb43e4b35fd8389c Author: Heng Li Date: Mon Feb 14 15:04:40 2011 -0500 change the default -k to 11 commit 07cf9d1e443d73cf053de38dd01671e3781f6e29 Author: Heng Li Date: Mon Feb 14 14:50:51 2011 -0500 sort fragments by vpos instead of by beg commit d0d3e7faabf5cbb7e5ff7b294f7e220da807c4c0 Author: Heng Li Date: Mon Feb 14 14:45:41 2011 -0500 shuffling the two haplotypes for better randomness commit 3be28eaf5f6033229aedf12ddb11a0084ba01cd8 Author: Heng Li Date: Mon Feb 14 14:09:17 2011 -0500 write chimeras to a separate BAM commit 80ccbc26f43918fe42be123cc1da9d3d7ce30816 Author: Heng Li Date: Mon Feb 14 13:54:13 2011 -0500 no mem leak/violation on small files; correctness is not checked commit 5c923867432fa14c26a19e3782e7f48d4080f6ac Author: Heng Li Date: Mon Feb 14 13:50:25 2011 -0500 bam separation; at least not immediate segfault commit cea2643ec30a59735bf89b2f562b563bf7263e79 Author: Heng Li Date: Sun Feb 13 23:24:11 2011 -0500 on the way to implement BAM separation; unfinished commit 964269cd15036a470ca89e43d0952201a0825671 Author: Heng Li Date: Sun Feb 13 18:07:56 2011 -0500 keep singletons in the hash table commit 2d4aa649bd670d5e038a1acaefd33c5fe24ae0e8 Author: Heng Li Date: Sun Feb 13 17:42:24 2011 -0500 Revert "prepare to add bam separation" This reverts commit ed6957e5211c2c4cf684dcb8bbb661052c74df6f. commit ed6957e5211c2c4cf684dcb8bbb661052c74df6f Author: Heng Li Date: Sun Feb 13 00:24:28 2011 -0500 prepare to add bam separation commit d211e652d93791d2e112d334added243ffe5fc3e Author: Heng Li Date: Sat Feb 12 18:50:20 2011 -0500 accelerate kstrtok commit 2d6af49d331ff5afe7b9e9b102e79d7d4512fdbe Author: Heng Li Date: Fri Feb 11 21:08:21 2011 -0500 split unlinked blocks commit 68e4cd1b560b0a6fd4c77e5e51eadde9fda26ea4 Author: Heng Li Date: Fri Feb 11 10:47:58 2011 -0500 remove heading and tailing ambiguous positions commit d2b685141426a902ae76660c1fbe8020da150cf8 Author: Heng Li Date: Fri Feb 11 10:02:21 2011 -0500 code clean up for further features commit c6980e062d55928b59f287c03e599dd5a37ed509 Author: Heng Li Date: Fri Feb 11 08:00:08 2011 -0500 change /64 to >>6; the latter is faster commit 91635b9c2687f24d72ee6a8aad2050a79bb8400f Merge: 41d4df2 9a7e155 Author: Heng Li Date: Fri Feb 11 01:22:55 2011 -0500 Merge branch 'master' into devel commit 9a7e155cc591c1b6c9f7f9cb939364a6becb65b2 Author: Heng Li Date: Fri Feb 11 01:21:07 2011 -0500 output an unrecognized field as '.'; autofix GL/PL commit 41d4df2e9545e9abe97151cfe5d6c763f3d00db1 Merge: c00c41c aacce0c Author: Heng Li Date: Thu Feb 10 23:00:14 2011 -0500 Merge branch 'master' into devel commit aacce0ce7276f451e4fddf81832f9e5f7f65198b Author: Heng Li Date: Thu Feb 10 22:57:53 2011 -0500 finished VCF->BCF conversion commit 0e875df643e41d848b709e2fa877de8ae53cdd4c Author: Heng Li Date: Thu Feb 10 21:57:28 2011 -0500 fixed a bug in reading VCF files commit c00c41c2a5da69cccea64adb542a0b365e56b4fc Author: Heng Li Date: Thu Feb 10 16:28:37 2011 -0500 suppres one-allele blocks commit 2e2354b673722e2f00d72970a043f80a66270da1 Author: Heng Li Date: Thu Feb 10 16:06:56 2011 -0500 fixed the bug in filtering commit d971e1fe24de4ecaf94055efffc5f641e2bdb563 Author: Heng Li Date: Thu Feb 10 12:24:23 2011 -0500 prepare to add filtering; buggy right now commit a0a5a3fbf504c3b02f7b9212e72315c1047cc249 Author: Heng Li Date: Thu Feb 10 11:55:02 2011 -0500 make masking optional commit 28db71ccd95054a5f8a47c2332794f8968f6a822 Author: Heng Li Date: Thu Feb 10 11:40:47 2011 -0500 routine to mask poorly called regions commit a3f6c439262bc10a4067860440f4d4dde9e0c515 Author: Heng Li Date: Wed Feb 9 17:18:33 2011 -0500 code clean up: remove globals commit 0b711978492f6ad39d459d78723c299468906818 Author: Heng Li Date: Wed Feb 9 16:52:54 2011 -0500 output more information commit f69d217ae5b691bf42ad07a97f29a7cc6456046f Author: Heng Li Date: Wed Feb 9 16:11:54 2011 -0500 fixed another bug in flipping commit d47882d549337fbcc251597508a2c7faf1bb92e2 Author: Heng Li Date: Wed Feb 9 16:01:35 2011 -0500 fixed a stupid bug in flipping commit e33f89de499496537f5fbde396a66557f0353f1b Author: Heng Li Date: Wed Feb 9 15:54:42 2011 -0500 fix chimeras; a little weird... commit 03d3c1d0b945245108ce0942d4772536a32212c7 Author: Heng Li Date: Wed Feb 9 13:27:35 2011 -0500 no effective change; prepare to fix chimera commit 6bc0a4676dd2252085a6e67bb06daa5ae05a554f Author: Heng Li Date: Wed Feb 9 11:52:58 2011 -0500 better count output commit dcac515439d25f71125d6de8111da417776ab9ce Author: Heng Li Date: Wed Feb 9 10:31:07 2011 -0500 prepare for another way of filtering commit ca7e4f1899b86d2e077994c789e8f69d699b3cd9 Author: Heng Li Date: Tue Feb 8 16:10:08 2011 -0500 fixed the bug; I can do better. commit 0733f77b98af121bdcb198cea6151d159831bb9c Author: Heng Li Date: Tue Feb 8 15:55:38 2011 -0500 fixed two bugs; still not working... commit 80f18cba9ba73c9592380fc1ecd53c351d294782 Author: Heng Li Date: Tue Feb 8 15:42:58 2011 -0500 filter false SNPs; NOT working right now commit 69a66e2f96d5b102cd712ff1527a3802fa84c590 Author: Heng Li Date: Tue Feb 8 14:39:09 2011 -0500 write sequence in the SAM format for debugging commit b6f1c9d160822af2b713be206f37bd6dde00546a Author: Heng Li Date: Mon Feb 7 11:51:21 2011 -0500 fixed two bugs commit 400aa5c06100af9c47cd5e4ce8b95b7deb84f54b Author: Heng Li Date: Mon Feb 7 11:22:38 2011 -0500 Optionally apply BAQ commit 4c82e0e19682e424f5cdb8381364114c307b329e Author: Heng Li Date: Mon Feb 7 01:23:31 2011 -0500 improved output; the result makes sense at a glance commit dc7853a581ab24bcc496e96b123ccf637e32ed1d Author: Heng Li Date: Sun Feb 6 14:12:43 2011 -0500 process per linked block instead of per chr commit e867d9c6c2e61d9e748e78163e5481dca5697a36 Author: Heng Li Date: Sun Feb 6 00:45:46 2011 -0500 DP seems to work on toy examples commit 445ad72fc43d4354d56f5f759790e8ae0be73d02 Author: Heng Li Date: Sat Feb 5 01:24:42 2011 -0500 implemented backtrack; not tested commit ba38e180b9cd545956583b22e97e09b4bb12073e Author: Heng Li Date: Fri Feb 4 23:55:23 2011 -0500 More "correct" DP; backtrack not implemented commit d69761fd9351273ccd37ea431b10509add91e7cf Author: Heng Li Date: Fri Feb 4 17:22:31 2011 -0500 scratch of dynamic programming; unfinished... commit 769ffcb44e26e59300791658801d321559b33858 Author: Heng Li Date: Fri Feb 4 16:29:55 2011 -0500 UNFINISHED commit. commit 9adab9591317c3467f3d8cdf2d19ec1f65d1b5b7 Author: Heng Li Date: Thu Feb 3 16:20:59 2011 -0500 another way of counting; can be even faster commit bbafbdc01ed1ceaab44927def1ad47c4c78aeb9c Author: Heng Li Date: Thu Feb 3 14:48:20 2011 -0500 for backup commit eba7446389cad62a19133bced1386a4334dcab79 Merge: a44a98e f01a593 Author: Heng Li Date: Wed Feb 2 14:06:07 2011 -0500 Merge branch 'master' into devel commit f01a5930445b5fda7e6b5b813ed63c652160ada2 Author: Heng Li Date: Wed Feb 2 11:31:54 2011 -0500 Better truncation warning when EOF is absent commit dd3ee5ed26c8bbef4a62fa5b2bfb0a75833f2c31 Author: Heng Li Date: Wed Feb 2 10:38:28 2011 -0500 fixed a typo in BCF/VCF headers commit b9d1137c55f401387113d1ad8a387489afe741db Author: Heng Li Date: Wed Feb 2 09:13:44 2011 -0500 fixed an out-of-boundary bug (fixed by Roel Kluin) commit a44a98e16559b9672e8a3492c8f8c640074b7ee2 Merge: ef68a14 d0443d5 Author: Heng Li Date: Tue Feb 1 21:54:48 2011 -0500 Merge branch 'master' into devel commit d0443d5c2f648e0f69bd4c56eaac7868e501c18b Author: Heng Li Date: Tue Feb 1 17:31:52 2011 -0500 improved sorting order checking commit ef68a14fab91399b2ecd38345936c3d6e7391cf3 Merge: 1e597b3 1a39a2e Author: Heng Li Date: Tue Feb 1 15:12:37 2011 -0500 Merge branch 'master' into devel commit 1a39a2eb08a270e20a34a0983e8bed6ffb3e2008 Author: Heng Li Date: Tue Feb 1 15:12:14 2011 -0500 more precise error message commit e028e7a47c02232e06a9dd3009262c00dede1060 Author: Heng Li Date: Tue Feb 1 14:48:01 2011 -0500 improved sorting order validation in index commit 1e597b3356744e2b791b12c9187f91c8054511d5 Author: Heng Li Date: Tue Feb 1 14:44:27 2011 -0500 testing only; not working commit 5753ace1e54228822d8ee95f69943f586e42f6e8 Author: Heng Li Date: Mon Jan 31 17:37:08 2011 -0500 reduce the effect of seq errors at the cost of SN commit 6f239ce5e0abd47babee33174476d48b723260d8 Author: Heng Li Date: Mon Jan 31 17:29:34 2011 -0500 added testing code commit 3db42fe22d27d61ab5735cd2308f73d93def8ebe Author: Heng Li Date: Mon Jan 31 14:33:21 2011 -0500 routine for phasing fosmid resequencing (incomplete) commit ed88f2797323229ae8f38fbcd107b231007956a8 Author: Heng Li Date: Mon Jan 31 10:12:53 2011 -0500 SAM output commit abc6acae28dc4794f6422255f077cf370d34e414 Merge: f1985a9 b133dbf Author: Heng Li Date: Sat Jan 29 22:56:10 2011 -0500 Merge branch 'master' into devel commit b133dbf82de4e8cea5eb56e5bbf0c4b3e9368fd5 Author: Heng Li Date: Sat Jan 29 22:37:11 2011 -0500 fixed a bug in tview on big-endian by Nathan Weeks commit 9d3fdaef29f91e21dbfcb9ff0165b9573e7c1042 Author: Heng Li Date: Sat Jan 29 22:24:00 2011 -0500 update INSTALL commit 9d074a38bde53961f96157b6fb3683b6dded38d7 Author: Heng Li Date: Sat Jan 29 21:56:25 2011 -0500 avoid a segfault when network connect fails commit f1985a93f7455b3ea1b0ef9b959d50b896ccd620 Author: Heng Li Date: Sat Jan 29 21:53:18 2011 -0500 fixed a bug about bit ordering commit d09797db6fef648a6823cbe718d67664660c6ebe Author: Heng Li Date: Thu Jan 27 16:53:19 2011 -0500 point out there are 4 or fewer free parameters commit 5fd1717650ed68ab6c55d094d1648c16a054891a Author: Heng Li Date: Thu Jan 27 16:09:18 2011 -0500 updated .gitignore commit fccb19fbe8f9de91f59d85bb49a248683dc6266c Author: Heng Li Date: Thu Jan 27 16:08:14 2011 -0500 fixed a bug; better scoring commit b4dcb844bde3d09eedcd9f6832186ece60ae5afd Merge: ffc3e89 6f502de Author: Heng Li Date: Thu Jan 27 14:50:30 2011 -0500 Merge branch 'master' into devel commit 6f502dec46b18dae4bb5b2319715d028b5e193d0 Author: Heng Li Date: Thu Jan 27 14:47:31 2011 -0500 skip unmapped and ref-skip reads in indel calling commit 3639f37dd8257b24560c35effcc3b6c16c3c1bcb Author: Heng Li Date: Thu Jan 27 14:19:15 2011 -0500 fixed an out-of-boundary bug in rare cases commit ffc3e89678ab9052b84f403da1e43044b045e73f Author: Heng Li Date: Thu Jan 27 14:00:17 2011 -0500 targetcut can be compiled, though probably buggy commit f452b3ac51306865ddde31a8d715b155d4d3e6e6 Author: Heng Li Date: Wed Jan 26 18:58:43 2011 -0500 this is for a very special application... commit ca1451c6406c7ee757cb31349ea0b8de70db0656 Author: Heng Li Date: Wed Jan 26 18:48:09 2011 -0500 fixed compiling errors commit 085b87a7642865f17239fb6a436e626e25417838 Author: Heng Li Date: Wed Jan 26 18:45:09 2011 -0500 This script was put in a wrong place... commit 090d360828622520de60385af4928ce1aebe0e48 Author: Heng Li Date: Wed Jan 26 18:33:58 2011 -0500 Imported from samtools-r902 ------------------------------------------------------------------------ r108 | lh3lh3 | 2009-01-20 11:56:45 +0000 (Tue, 20 Jan 2009) | 2 lines Changed paths: M /branches/dev/samtools/examples/Makefile made it a little more convenient ------------------------------------------------------------------------ r107 | lh3lh3 | 2009-01-20 11:53:30 +0000 (Tue, 20 Jan 2009) | 2 lines Changed paths: A /branches/dev/samtools/examples/Makefile added a Makefile ------------------------------------------------------------------------ r106 | lh3lh3 | 2009-01-20 11:25:05 +0000 (Tue, 20 Jan 2009) | 2 lines Changed paths: M /branches/dev/samtools/misc/maq2sam.c support RG tag ------------------------------------------------------------------------ r105 | lh3lh3 | 2009-01-18 17:37:20 +0000 (Sun, 18 Jan 2009) | 2 lines Changed paths: M /branches/dev/samtools/ChangeLog update changelog ------------------------------------------------------------------------ r104 | lh3lh3 | 2009-01-18 17:31:21 +0000 (Sun, 18 Jan 2009) | 3 lines Changed paths: M /branches/dev/samtools/bam.h M /branches/dev/samtools/bam_lpileup.c M /branches/dev/samtools/bamtk.c * samtools-0.1.1-18 * fixed a bug in bam_lpileup.c: segment start and end are not correctly recognized ------------------------------------------------------------------------ r103 | lh3lh3 | 2009-01-18 16:34:03 +0000 (Sun, 18 Jan 2009) | 5 lines Changed paths: M /branches/dev/samtools/bam_import.c M /branches/dev/samtools/bam_index.c M /branches/dev/samtools/bamtk.c * samtools-0.1.1-17 * fixed a bug when there are reads without coordinates * also recognize type 'c' as 'A' * found a bug in bam_lpileup.c; NOT fixed yet ------------------------------------------------------------------------ r102 | lh3lh3 | 2009-01-17 19:46:49 +0000 (Sat, 17 Jan 2009) | 2 lines Changed paths: A /branches/dev/samtools/INSTALL Instruction for compilation ------------------------------------------------------------------------ r101 | lh3lh3 | 2009-01-17 19:31:36 +0000 (Sat, 17 Jan 2009) | 3 lines Changed paths: M /branches/dev/samtools/Makefile A /branches/dev/samtools/Makefile.lite M /branches/dev/samtools/bam.h M /branches/dev/samtools/faidx.c M /branches/dev/samtools/misc/Makefile M /branches/dev/samtools/razf.c * replaced HAVE_RAZF with _NO_RAZF * added Makefile.lite for people who have trouble with razf.c ------------------------------------------------------------------------ r100 | lh3lh3 | 2009-01-16 10:03:37 +0000 (Fri, 16 Jan 2009) | 3 lines Changed paths: M /branches/dev/samtools/bam_mate.c M /branches/dev/samtools/bamtk.c M /branches/dev/samtools/misc/wgsim.c * samtools-0.1.1-15 * fixed another bug in fixmate: unmapped pair has non-zero isize ------------------------------------------------------------------------ r99 | lh3lh3 | 2009-01-16 09:13:36 +0000 (Fri, 16 Jan 2009) | 4 lines Changed paths: M /branches/dev/samtools/ChangeLog M /branches/dev/samtools/bam_mate.c M /branches/dev/samtools/bamtk.c * samtools-0.1.1-14 * fixed a bug in fixmate: isize not equal to zero if two ends mapped to different chr ------------------------------------------------------------------------ r98 | lh3lh3 | 2009-01-15 16:47:41 +0000 (Thu, 15 Jan 2009) | 3 lines Changed paths: M /branches/dev/samtools/bam_maqcns.c M /branches/dev/samtools/bamtk.c * samtools-0.1.1-13 * fixed the prior for hom indels (Richard pointed this out) ------------------------------------------------------------------------ r97 | lh3lh3 | 2009-01-15 16:38:47 +0000 (Thu, 15 Jan 2009) | 4 lines Changed paths: M /branches/dev/samtools/COPYING M /branches/dev/samtools/bam_sort.c M /branches/dev/samtools/bamtk.c M /branches/dev/samtools/source.dot * samtools-0.1.1-12 * fixed a bug in sort * update source file graph and copyright information ------------------------------------------------------------------------ r96 | lh3lh3 | 2009-01-14 21:46:14 +0000 (Wed, 14 Jan 2009) | 2 lines Changed paths: M /branches/dev/samtools/glf.c fixed a typo ------------------------------------------------------------------------ r95 | lh3lh3 | 2009-01-14 21:44:53 +0000 (Wed, 14 Jan 2009) | 2 lines Changed paths: M /branches/dev/samtools/glf.c added a main function for glf.c ------------------------------------------------------------------------ r94 | lh3lh3 | 2009-01-14 17:14:59 +0000 (Wed, 14 Jan 2009) | 4 lines Changed paths: M /branches/dev/samtools/Makefile M /branches/dev/samtools/bam_plcmd.c M /branches/dev/samtools/bamtk.c M /branches/dev/samtools/bgzf.h A /branches/dev/samtools/glf.c M /branches/dev/samtools/glf.h * samtools-0.1.1-11 * generate binary GLFv2 * added glfview command to dump GLFv2 binary file ------------------------------------------------------------------------ r93 | lh3lh3 | 2009-01-14 15:07:44 +0000 (Wed, 14 Jan 2009) | 4 lines Changed paths: M /branches/dev/samtools/bam_rmdup.c M /branches/dev/samtools/bamtk.c M /branches/dev/samtools/glf.h * samtools-0.1.1-10 * fixed several bugs in rmdup * prepare to generate GLF2 ------------------------------------------------------------------------ r92 | lh3lh3 | 2009-01-14 13:27:44 +0000 (Wed, 14 Jan 2009) | 3 lines Changed paths: M /branches/dev/samtools/Makefile M /branches/dev/samtools/bam.h M /branches/dev/samtools/bam_import.c A /branches/dev/samtools/bam_rmdup.c M /branches/dev/samtools/bamtk.c * samtools-0.1.1-9 * implemented rmdup; NOT tested yet ------------------------------------------------------------------------ r91 | lh3lh3 | 2009-01-13 20:15:43 +0000 (Tue, 13 Jan 2009) | 2 lines Changed paths: M /branches/dev/samtools/examples/00README.txt update README for typos ------------------------------------------------------------------------ r90 | lh3lh3 | 2009-01-13 19:57:50 +0000 (Tue, 13 Jan 2009) | 2 lines Changed paths: M /branches/dev/samtools/examples/ex1.sam.gz update example ------------------------------------------------------------------------ r89 | lh3lh3 | 2009-01-13 17:21:38 +0000 (Tue, 13 Jan 2009) | 3 lines Changed paths: M /branches/dev/samtools/Makefile M /branches/dev/samtools/bam.c A /branches/dev/samtools/bam_mate.c M /branches/dev/samtools/bamtk.c * samtools-0.1.1-8 * added fixmate command ------------------------------------------------------------------------ r88 | lh3lh3 | 2009-01-13 10:48:23 +0000 (Tue, 13 Jan 2009) | 3 lines Changed paths: M /branches/dev/samtools/bam_plcmd.c M /branches/dev/samtools/bamtk.c * samtools-0.1.1-7 * change the reported indel position to the previous way ------------------------------------------------------------------------ r87 | lh3lh3 | 2009-01-12 22:12:12 +0000 (Mon, 12 Jan 2009) | 4 lines Changed paths: M /branches/dev/samtools/bam_plcmd.c M /branches/dev/samtools/bamtk.c * samtools-0.1.1-6 * addd glt output * allow to change indel calling parameters at the command line ------------------------------------------------------------------------ r86 | lh3lh3 | 2009-01-12 21:16:48 +0000 (Mon, 12 Jan 2009) | 4 lines Changed paths: M /branches/dev/samtools/bam.h M /branches/dev/samtools/bam_pileup.c M /branches/dev/samtools/bam_plcmd.c M /branches/dev/samtools/bamtk.c * samtools-0.1.1-5 * added two more flags * allowed to select reads shown in pileup with a mask ------------------------------------------------------------------------ r85 | lh3lh3 | 2009-01-12 20:47:51 +0000 (Mon, 12 Jan 2009) | 4 lines Changed paths: M /branches/dev/samtools/bam_index.c M /branches/dev/samtools/bam_plcmd.c M /branches/dev/samtools/bamtk.c * samtools-0.1.1-4 * fixed a bug in indexing (linear index) * prepare to add glt output from pileup ------------------------------------------------------------------------ r84 | lh3lh3 | 2009-01-12 09:22:35 +0000 (Mon, 12 Jan 2009) | 3 lines Changed paths: M /branches/dev/samtools/bam_plcmd.c M /branches/dev/samtools/bamtk.c * samtools-0.1.1-3 * fixed a bug in outputing the coordinate of an indel ------------------------------------------------------------------------ r83 | lh3lh3 | 2009-01-11 15:18:01 +0000 (Sun, 11 Jan 2009) | 3 lines Changed paths: M /branches/dev/samtools/bam_plcmd.c M /branches/dev/samtools/bamtk.c * samtools-0.1.1-2 * pileup: allows to output indel sites only ------------------------------------------------------------------------ r82 | lh3lh3 | 2009-01-10 23:34:31 +0000 (Sat, 10 Jan 2009) | 3 lines Changed paths: M /branches/dev/samtools/bam_maqcns.c M /branches/dev/samtools/bam_maqcns.h M /branches/dev/samtools/bam_plcmd.c M /branches/dev/samtools/bamtk.c * samtools-0.1.1-1 * implemented a Bayesian indel caller ------------------------------------------------------------------------ r81 | lh3lh3 | 2009-01-09 09:54:28 +0000 (Fri, 09 Jan 2009) | 2 lines Changed paths: M /branches/dev/samtools/examples/00README.txt D /branches/dev/samtools/examples/ex1.fa.fai Let users generate ex1.fa.fai. ------------------------------------------------------------------------ r80 | lh3lh3 | 2009-01-08 16:10:08 +0000 (Thu, 08 Jan 2009) | 2 lines Changed paths: M /branches/dev/samtools/misc/bowtie2sam.pl make the bowtie converter works for "-k 2" ------------------------------------------------------------------------ r78 | lh3lh3 | 2009-01-03 17:25:24 +0000 (Sat, 03 Jan 2009) | 2 lines Changed paths: M /branches/dev/samtools/misc/export2sam.pl fixed a bug for "QC" reads ------------------------------------------------------------------------ r77 | lh3lh3 | 2009-01-01 18:32:06 +0000 (Thu, 01 Jan 2009) | 3 lines Changed paths: A /branches/dev/samtools/misc/bowtie2sam.pl M /branches/dev/samtools/misc/soap2sam.pl * soap2sam.pl: added NM tag * bowtie2sam.pl: converter for bowtie ------------------------------------------------------------------------ r76 | lh3lh3 | 2008-12-31 23:24:24 +0000 (Wed, 31 Dec 2008) | 2 lines Changed paths: A /branches/dev/samtools/misc/soap2sam.pl soap2sam.pl: convert soap output to SAM ------------------------------------------------------------------------ r75 | lh3lh3 | 2008-12-31 17:54:32 +0000 (Wed, 31 Dec 2008) | 3 lines Changed paths: M /branches/dev/samtools/misc/wgsim_eval.pl * wgsim_eval.pl-0.1.1 * fixed a bug for a contig name like "NT_012345" ------------------------------------------------------------------------ r74 | lh3lh3 | 2008-12-31 16:38:21 +0000 (Wed, 31 Dec 2008) | 2 lines Changed paths: A /branches/dev/samtools/misc/wgsim_eval.pl * evaluate alignment for reads generated by wgsim ------------------------------------------------------------------------ r73 | lh3lh3 | 2008-12-31 15:11:22 +0000 (Wed, 31 Dec 2008) | 2 lines Changed paths: M /branches/dev/samtools/misc/Makefile M /branches/dev/samtools/misc/wgsim.c fixed compiling warnings for wgsim ------------------------------------------------------------------------ r72 | lh3lh3 | 2008-12-31 13:40:51 +0000 (Wed, 31 Dec 2008) | 2 lines Changed paths: M /branches/dev/samtools/bam_tview.c remove an unused variable (a compiler warning only) ------------------------------------------------------------------------ r71 | lh3lh3 | 2008-12-31 13:37:16 +0000 (Wed, 31 Dec 2008) | 2 lines Changed paths: M /branches/dev/samtools/misc/Makefile A /branches/dev/samtools/misc/wgsim.c wgsim: Paired-end reads simulator ------------------------------------------------------------------------ r70 | bhandsaker | 2008-12-29 20:27:16 +0000 (Mon, 29 Dec 2008) | 2 lines Changed paths: M /branches/dev/samtools/bam_maqcns.c M /branches/dev/samtools/bam_tview.c Move definition of bam_nt16_nt4_table so we can build without curses. ------------------------------------------------------------------------ r62 | lh3lh3 | 2008-12-22 15:55:13 +0000 (Mon, 22 Dec 2008) | 2 lines Changed paths: A /branches/dev/samtools/NEWS M /branches/dev/samtools/bamtk.c M /branches/dev/samtools/samtools.1 Release samtools-0.1.1 ------------------------------------------------------------------------ r61 | lh3lh3 | 2008-12-22 15:46:08 +0000 (Mon, 22 Dec 2008) | 10 lines Changed paths: M /branches/dev/samtools/bam_aux.c M /branches/dev/samtools/bam_index.c M /branches/dev/samtools/bam_plcmd.c M /branches/dev/samtools/bam_tview.c M /branches/dev/samtools/bamtk.c M /branches/dev/samtools/razf.c M /branches/dev/samtools/samtools.1 * samtools-0.1.0-66 * fixed a bug in razf.c: reset z_eof when razf_seek() is called * fixed a memory leak in parsing a region * changed pileup a little bit when -s is in use: output ^ and $ * when a bam is not indexed, output more meaningful error message * fixed a bug in indexing for small alignment * fixed a bug in the viewer when we come to the end of a reference file * updated documentation * prepare to release 0.1.1 ------------------------------------------------------------------------ r60 | lh3lh3 | 2008-12-22 15:10:16 +0000 (Mon, 22 Dec 2008) | 2 lines Changed paths: A /branches/dev/samtools/examples A /branches/dev/samtools/examples/00README.txt A /branches/dev/samtools/examples/ex1.fa A /branches/dev/samtools/examples/ex1.fa.fai A /branches/dev/samtools/examples/ex1.sam.gz example ------------------------------------------------------------------------ r59 | lh3lh3 | 2008-12-22 09:38:15 +0000 (Mon, 22 Dec 2008) | 2 lines Changed paths: M /branches/dev/samtools/ChangeLog update ChangeLog ------------------------------------------------------------------------ r58 | lh3lh3 | 2008-12-20 23:06:00 +0000 (Sat, 20 Dec 2008) | 3 lines Changed paths: M /branches/dev/samtools/misc/export2sam.pl * added comments * fixed several bugs ------------------------------------------------------------------------ r57 | lh3lh3 | 2008-12-20 15:44:20 +0000 (Sat, 20 Dec 2008) | 2 lines Changed paths: A /branches/dev/samtools/misc/export2sam.pl convert Export format to SAM; not thoroughly tested ------------------------------------------------------------------------ r56 | lh3lh3 | 2008-12-19 22:13:28 +0000 (Fri, 19 Dec 2008) | 6 lines Changed paths: M /branches/dev/samtools/bam_import.c M /branches/dev/samtools/bam_plcmd.c M /branches/dev/samtools/bam_tview.c M /branches/dev/samtools/bamtk.c A /branches/dev/samtools/source.dot * samtools-0.1.0-65 * pileup: generate maq-like simple output * pileup: allow to output pileup at required sites * source.dot: source file relationship graph * tview: fixed a minor bug ------------------------------------------------------------------------ r55 | lh3lh3 | 2008-12-19 20:10:26 +0000 (Fri, 19 Dec 2008) | 2 lines Changed paths: D /branches/dev/samtools/misc/all2sam.pl remove all2sam.pl ------------------------------------------------------------------------ r54 | lh3lh3 | 2008-12-16 22:34:25 +0000 (Tue, 16 Dec 2008) | 2 lines Changed paths: A /branches/dev/samtools/COPYING M /branches/dev/samtools/bam.h M /branches/dev/samtools/faidx.h M /branches/dev/samtools/khash.h M /branches/dev/samtools/kseq.h M /branches/dev/samtools/ksort.h M /branches/dev/samtools/samtools.1 Added copyright information and a bit more documentation. No code change. ------------------------------------------------------------------------ r53 | lh3lh3 | 2008-12-16 13:40:18 +0000 (Tue, 16 Dec 2008) | 3 lines Changed paths: M /branches/dev/samtools/bam.c M /branches/dev/samtools/bam.h M /branches/dev/samtools/bam_index.c M /branches/dev/samtools/bam_maqcns.c M /branches/dev/samtools/bamtk.c * samtools-0.1.0-64 * improved efficiency of the indel caller for spliced alignments ------------------------------------------------------------------------ r52 | lh3lh3 | 2008-12-16 10:28:20 +0000 (Tue, 16 Dec 2008) | 3 lines Changed paths: M /branches/dev/samtools/bam.c M /branches/dev/samtools/bam.h M /branches/dev/samtools/bam_aux.c M /branches/dev/samtools/bam_index.c M /branches/dev/samtools/bamtk.c * samtools-0.1.0-63 * a bit code cleanup: reduce the dependency between source files ------------------------------------------------------------------------ r51 | lh3lh3 | 2008-12-15 14:29:32 +0000 (Mon, 15 Dec 2008) | 3 lines Changed paths: M /branches/dev/samtools/bam_maqcns.c M /branches/dev/samtools/bam_plcmd.c M /branches/dev/samtools/bamtk.c * samtools-0.1.0-62 * fixed a memory leak ------------------------------------------------------------------------ r50 | lh3lh3 | 2008-12-15 14:00:13 +0000 (Mon, 15 Dec 2008) | 2 lines Changed paths: M /branches/dev/samtools/ChangeLog M /branches/dev/samtools/bam.h M /branches/dev/samtools/samtools.1 update documentation, ChangeLog and a comment ------------------------------------------------------------------------ r49 | lh3lh3 | 2008-12-15 13:36:43 +0000 (Mon, 15 Dec 2008) | 6 lines Changed paths: M /branches/dev/samtools/Makefile M /branches/dev/samtools/bam.h M /branches/dev/samtools/bam_maqcns.c M /branches/dev/samtools/bam_maqcns.h M /branches/dev/samtools/bam_pileup.c A /branches/dev/samtools/bam_plcmd.c M /branches/dev/samtools/bamtk.c M /branches/dev/samtools/samtools.1 * samtools-0.1.0-61 * moved pileup command to a separate source file * added indel caller * added bam_cal_segend(). (NOT WORKING for spliced alignment!!!) * updated documentation ------------------------------------------------------------------------ r48 | lh3lh3 | 2008-12-12 13:55:36 +0000 (Fri, 12 Dec 2008) | 3 lines Changed paths: M /branches/dev/samtools/bam_maqcns.c M /branches/dev/samtools/bamtk.c * samtools-0.1.0-60 * fixed another bug in maqcns when there is a nearby deletion ------------------------------------------------------------------------ r47 | lh3lh3 | 2008-12-12 13:42:16 +0000 (Fri, 12 Dec 2008) | 5 lines Changed paths: M /branches/dev/samtools/bam_maqcns.c M /branches/dev/samtools/bam_pileup.c M /branches/dev/samtools/bamtk.c * samtools-0.1.0-59 * pileup: outputing consensus is now optional * fixed a bug in glfgen. This bug also exists in maq's glfgen. However, I am not quite sure why the previous version may have problem. ------------------------------------------------------------------------ r46 | lh3lh3 | 2008-12-12 11:44:56 +0000 (Fri, 12 Dec 2008) | 6 lines Changed paths: M /branches/dev/samtools/bam_pileup.c M /branches/dev/samtools/bamtk.c * samtools-0.1.0-58 * add maq consensus to pileup. However, I will move this part to a new command as strictly speaking, consensus callin is not part of pileup, and imposing it would make it harder to generate for other language bindings. ------------------------------------------------------------------------ r45 | bhandsaker | 2008-12-11 20:43:56 +0000 (Thu, 11 Dec 2008) | 2 lines Changed paths: M /branches/dev/samtools/bgzf.c Fix bug in tell() after reads that consume to the exact end of a block. ------------------------------------------------------------------------ r44 | lh3lh3 | 2008-12-11 09:36:53 +0000 (Thu, 11 Dec 2008) | 2 lines Changed paths: M /branches/dev/samtools/samtools.1 update manual ------------------------------------------------------------------------ r43 | lh3lh3 | 2008-12-11 09:25:36 +0000 (Thu, 11 Dec 2008) | 4 lines Changed paths: M /branches/dev/samtools/bam_import.c M /branches/dev/samtools/bamtk.c * samtools-0.1.0-57 * fixed a bug in parser when there is auxiliary fields * made the parser a bit more robust ------------------------------------------------------------------------ r42 | lh3lh3 | 2008-12-10 14:57:29 +0000 (Wed, 10 Dec 2008) | 5 lines Changed paths: M /branches/dev/samtools/bam_index.c M /branches/dev/samtools/bamtk.c M /branches/dev/samtools/bgzf.c * samtools-0.1.0-56 * fixed a bug in bgzf (only reading is affected) * fixed a typo in bam_index.c * in bam_index.c, check potential bugs in the underlying I/O library ------------------------------------------------------------------------ r41 | lh3lh3 | 2008-12-10 12:53:08 +0000 (Wed, 10 Dec 2008) | 2 lines Changed paths: M /branches/dev/samtools/samtools.1 update manual ------------------------------------------------------------------------ r40 | lh3lh3 | 2008-12-10 11:52:10 +0000 (Wed, 10 Dec 2008) | 5 lines Changed paths: M /branches/dev/samtools/bam.h M /branches/dev/samtools/bam_pileup.c M /branches/dev/samtools/bamtk.c * samtools-0.1.0-55 * tried to make pileup work with clipping (previously not), though NOT tested * removed -v from pileup * made pileup take the reference sequence ------------------------------------------------------------------------ r39 | lh3lh3 | 2008-12-09 11:59:28 +0000 (Tue, 09 Dec 2008) | 4 lines Changed paths: M /branches/dev/samtools/bam_import.c M /branches/dev/samtools/bamtk.c M /branches/dev/samtools/samtools.1 * samtools-0.1.0-54 * in parser, recognize "=", rather than ",", as a match * in parser, correctl parse "=" at the MRNM field. ------------------------------------------------------------------------ r38 | lh3lh3 | 2008-12-09 11:39:07 +0000 (Tue, 09 Dec 2008) | 2 lines Changed paths: M /branches/dev/samtools/misc/maq2sam.c fixed a bug in handling maq flag 64 and 192 ------------------------------------------------------------------------ r37 | lh3lh3 | 2008-12-09 09:53:46 +0000 (Tue, 09 Dec 2008) | 2 lines Changed paths: M /branches/dev/samtools/misc/md5fa.c also calculate unordered md5sum check ------------------------------------------------------------------------ r36 | lh3lh3 | 2008-12-09 09:46:21 +0000 (Tue, 09 Dec 2008) | 2 lines Changed paths: M /branches/dev/samtools/misc/md5fa.c fixed a minor bug when there are space in the sequence ------------------------------------------------------------------------ r35 | lh3lh3 | 2008-12-09 09:40:45 +0000 (Tue, 09 Dec 2008) | 2 lines Changed paths: M /branches/dev/samtools/misc/md5fa.c fixed a potential memory leak ------------------------------------------------------------------------ r34 | lh3lh3 | 2008-12-08 14:52:17 +0000 (Mon, 08 Dec 2008) | 2 lines Changed paths: M /branches/dev/samtools/bam_import.c M /branches/dev/samtools/bam_index.c M /branches/dev/samtools/bamtk.c * fixed a bug in import: bin is wrongly calculated ------------------------------------------------------------------------ r33 | lh3lh3 | 2008-12-08 14:08:01 +0000 (Mon, 08 Dec 2008) | 2 lines Changed paths: M /branches/dev/samtools/misc/all2sam.pl nothing, really ------------------------------------------------------------------------ r32 | lh3lh3 | 2008-12-08 12:56:02 +0000 (Mon, 08 Dec 2008) | 3 lines Changed paths: M /branches/dev/samtools/Makefile M /branches/dev/samtools/kseq.h M /branches/dev/samtools/misc/Makefile A /branches/dev/samtools/misc/md5.c A /branches/dev/samtools/misc/md5.h A /branches/dev/samtools/misc/md5fa.c * fixed two warnings in kseq.h * added md5sum utilities ------------------------------------------------------------------------ r31 | lh3lh3 | 2008-12-08 11:35:29 +0000 (Mon, 08 Dec 2008) | 5 lines Changed paths: M /branches/dev/samtools/Makefile M /branches/dev/samtools/bam_import.c M /branches/dev/samtools/bamtk.c A /branches/dev/samtools/kseq.h D /branches/dev/samtools/kstream.h * samtools-0.1.0-52 * replace kstream with kseq. kseq is a superset of kstream. I need the extra functions in kseq.h. * also compile stand-alone faidx ------------------------------------------------------------------------ r30 | lh3lh3 | 2008-12-08 11:17:04 +0000 (Mon, 08 Dec 2008) | 3 lines Changed paths: M /branches/dev/samtools/bam.h M /branches/dev/samtools/bam_sort.c M /branches/dev/samtools/bamtk.c * samtools-0.1.0-51 * sorting by read names is available ------------------------------------------------------------------------ r29 | lh3lh3 | 2008-12-08 10:29:02 +0000 (Mon, 08 Dec 2008) | 3 lines Changed paths: M /branches/dev/samtools/bam.c M /branches/dev/samtools/bam.h M /branches/dev/samtools/bam_import.c M /branches/dev/samtools/bam_maqcns.c M /branches/dev/samtools/bam_pileup.c M /branches/dev/samtools/bam_sort.c M /branches/dev/samtools/bam_tview.c M /branches/dev/samtools/bamtk.c M /branches/dev/samtools/misc/maq2sam.c * samtools-0.1.0-50 * format change to meet the latest specification ------------------------------------------------------------------------ r28 | lh3lh3 | 2008-12-04 16:09:21 +0000 (Thu, 04 Dec 2008) | 3 lines Changed paths: M /branches/dev/samtools/bam_maqcns.c M /branches/dev/samtools/misc/maq2sam.c * minor change in maqcns: special care when n==0 * change maq2sam to meet the latest specification ------------------------------------------------------------------------ r27 | lh3lh3 | 2008-12-04 15:55:44 +0000 (Thu, 04 Dec 2008) | 2 lines Changed paths: M /branches/dev/samtools/razf.c M /branches/dev/samtools/razf.h considerable code clean up in razf ------------------------------------------------------------------------ r26 | lh3lh3 | 2008-12-04 15:08:18 +0000 (Thu, 04 Dec 2008) | 2 lines Changed paths: M /branches/dev/samtools/ChangeLog M /branches/dev/samtools/Makefile M /branches/dev/samtools/faidx.c make RAZF optional in faidx.c ------------------------------------------------------------------------ r25 | lh3lh3 | 2008-12-01 15:27:22 +0000 (Mon, 01 Dec 2008) | 3 lines Changed paths: M /branches/dev/samtools/Makefile M /branches/dev/samtools/bam.h M /branches/dev/samtools/bam_aux.c M /branches/dev/samtools/bamtk.c M /branches/dev/samtools/samtools.1 * samtools-0.1.0-49 * added routines for retrieving aux data, NOT TESTED YET! ------------------------------------------------------------------------ r24 | lh3lh3 | 2008-12-01 14:29:43 +0000 (Mon, 01 Dec 2008) | 5 lines Changed paths: M /branches/dev/samtools/bam.c M /branches/dev/samtools/bam_import.c M /branches/dev/samtools/bam_maqcns.c M /branches/dev/samtools/bamtk.c M /branches/dev/samtools/bgzf.c M /branches/dev/samtools/samtools.1 * samtools-0.1.0-48 * bgzf: fixed a potential integer overflow on 32-it machines * maqcns: set the minimum combined quality as 0 * supporting hex strings ------------------------------------------------------------------------ r23 | lh3lh3 | 2008-11-27 17:14:37 +0000 (Thu, 27 Nov 2008) | 3 lines Changed paths: M /branches/dev/samtools/bam_maqcns.c M /branches/dev/samtools/bamtk.c * samtools-0.1.0-47 * fixed the bug in maqcns ------------------------------------------------------------------------ r22 | lh3lh3 | 2008-11-27 17:08:11 +0000 (Thu, 27 Nov 2008) | 3 lines Changed paths: M /branches/dev/samtools/Makefile M /branches/dev/samtools/bam.h A /branches/dev/samtools/bam_maqcns.c A /branches/dev/samtools/bam_maqcns.h M /branches/dev/samtools/bam_tview.c M /branches/dev/samtools/bamtk.c A /branches/dev/samtools/glf.h * samtools-0.1.0-46 * add MAQ consensus caller, currently BUGGY! ------------------------------------------------------------------------ r21 | lh3lh3 | 2008-11-27 13:51:28 +0000 (Thu, 27 Nov 2008) | 4 lines Changed paths: M /branches/dev/samtools/bam_pileup.c M /branches/dev/samtools/bam_tview.c M /branches/dev/samtools/bamtk.c * samtools-0.1.0-45 * tview: display padded alignment (but not P operation) * better coordinates and reference sequence ------------------------------------------------------------------------ r19 | lh3lh3 | 2008-11-27 09:26:05 +0000 (Thu, 27 Nov 2008) | 2 lines Changed paths: A /branches/dev/samtools/ChangeLog new ChangeLog ------------------------------------------------------------------------ r18 | lh3lh3 | 2008-11-27 09:24:45 +0000 (Thu, 27 Nov 2008) | 3 lines Changed paths: D /branches/dev/samtools/ChangeLog A /branches/dev/samtools/ChangeLog.old (from /branches/dev/samtools/ChangeLog:6) Rename ChangeLog to ChangeLog.old. This old ChangeLog is generated from the log of my personal SVN repository. ------------------------------------------------------------------------ r17 | lh3lh3 | 2008-11-27 09:22:55 +0000 (Thu, 27 Nov 2008) | 6 lines Changed paths: M /branches/dev/samtools/Makefile M /branches/dev/samtools/bamtk.c M /branches/dev/samtools/bgzf.c * samtools-0.1.0-44 * declare fseeko and ftello as some Linux may not do this by default and missing these declarations will make bgzf buggy * get rid of some harmless warings * use BGZF by default, now ------------------------------------------------------------------------ r16 | lh3lh3 | 2008-11-26 21:19:11 +0000 (Wed, 26 Nov 2008) | 4 lines Changed paths: M /branches/dev/samtools/bam_index.c M /branches/dev/samtools/bamtk.c M /branches/dev/samtools/razf.c * samtools-0.1.0-43 * fixed a bug in razf_read() * give more warnings when the file is truncated (or due to bugs in I/O library) ------------------------------------------------------------------------ r15 | lh3lh3 | 2008-11-26 20:41:39 +0000 (Wed, 26 Nov 2008) | 2 lines Changed paths: M /branches/dev/samtools/bgzf.c fixed a bug in bgzf.c at the end of the file ------------------------------------------------------------------------ r14 | lh3lh3 | 2008-11-26 17:05:18 +0000 (Wed, 26 Nov 2008) | 4 lines Changed paths: M /branches/dev/samtools/bamtk.c * samtools-0.1.0-42 * a lot happened to RAZF, although samtools itself is untouched. Better also update the version number anyway to avoid confusion ------------------------------------------------------------------------ r13 | lh3lh3 | 2008-11-26 17:03:48 +0000 (Wed, 26 Nov 2008) | 2 lines Changed paths: M /branches/dev/samtools/razf.c a change from Jue, but I think it should not matter ------------------------------------------------------------------------ r12 | lh3lh3 | 2008-11-26 16:48:14 +0000 (Wed, 26 Nov 2008) | 3 lines Changed paths: M /branches/dev/samtools/razf.c fixed a potential bug in razf. However, it seems still buggy, just rarely happens, very rarely. ------------------------------------------------------------------------ r11 | lh3lh3 | 2008-11-26 14:02:56 +0000 (Wed, 26 Nov 2008) | 2 lines Changed paths: M /branches/dev/samtools/razf.c fixed a bug in razf, with the help of Jue ------------------------------------------------------------------------ r10 | lh3lh3 | 2008-11-26 11:55:32 +0000 (Wed, 26 Nov 2008) | 2 lines Changed paths: M /branches/dev/samtools/bam_index.c remove a comment ------------------------------------------------------------------------ r9 | lh3lh3 | 2008-11-26 11:37:05 +0000 (Wed, 26 Nov 2008) | 2 lines Changed paths: M /branches/dev/samtools/Makefile M /branches/dev/samtools/bam.h M /branches/dev/samtools/razf.c M /branches/dev/samtools/razf.h * Jue has updated razf to realize Bob's scheme ------------------------------------------------------------------------ r7 | lh3lh3 | 2008-11-25 20:37:37 +0000 (Tue, 25 Nov 2008) | 2 lines Changed paths: A /branches/dev/samtools/samtools.1 the manual page ------------------------------------------------------------------------ r6 | lh3lh3 | 2008-11-25 20:37:16 +0000 (Tue, 25 Nov 2008) | 3 lines Changed paths: A /branches/dev/samtools/ChangeLog A /branches/dev/samtools/Makefile A /branches/dev/samtools/bam.c A /branches/dev/samtools/bam.h A /branches/dev/samtools/bam_aux.c A /branches/dev/samtools/bam_endian.h A /branches/dev/samtools/bam_import.c A /branches/dev/samtools/bam_index.c A /branches/dev/samtools/bam_lpileup.c A /branches/dev/samtools/bam_pileup.c A /branches/dev/samtools/bam_sort.c A /branches/dev/samtools/bam_tview.c A /branches/dev/samtools/bamtk.c A /branches/dev/samtools/bgzf.c A /branches/dev/samtools/bgzf.h A /branches/dev/samtools/bgzip.c A /branches/dev/samtools/faidx.c A /branches/dev/samtools/faidx.h A /branches/dev/samtools/khash.h A /branches/dev/samtools/ksort.h A /branches/dev/samtools/kstream.h A /branches/dev/samtools/misc A /branches/dev/samtools/misc/Makefile A /branches/dev/samtools/misc/all2sam.pl A /branches/dev/samtools/misc/maq2sam.c A /branches/dev/samtools/razf.c A /branches/dev/samtools/razf.h A /branches/dev/samtools/razip.c A /branches/dev/samtools/zutil.h The initial version of samtools, replicated from my local SVN repository. The current version is: 0.1.0-42. All future development will happen here. ------------------------------------------------------------------------ r5 | lh3lh3 | 2008-11-25 20:30:49 +0000 (Tue, 25 Nov 2008) | 2 lines Changed paths: A /branches/dev/samtools samtools (C version) ------------------------------------------------------------------------ ------------------------------------------------------------------------ r703 | lh3 | 2008-11-25 20:20:02 +0000 (Tue, 25 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/samtools.1 rename bamtk to samtools ------------------------------------------------------------------------ r702 | lh3 | 2008-11-25 20:15:09 +0000 (Tue, 25 Nov 2008) | 2 lines Changed paths: D /branches/prog/bam/bamtk.1 A /branches/prog/bam/samtools.1 (from /branches/prog/bam/bamtk.1:679) rename bamtk.1 to samtools.1 ------------------------------------------------------------------------ r701 | lh3 | 2008-11-25 13:29:10 +0000 (Tue, 25 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/Makefile M /branches/prog/bam/bam.c M /branches/prog/bam/bam.h M /branches/prog/bam/bam_import.c M /branches/prog/bam/bam_index.c M /branches/prog/bam/bam_pileup.c M /branches/prog/bam/bamtk.c M /branches/prog/bam/misc/Makefile * samtools-0.1.0-41 * small (but a bit dangerous) changes to meet the latest specification ------------------------------------------------------------------------ r700 | lh3 | 2008-11-25 13:15:11 +0000 (Tue, 25 Nov 2008) | 2 lines Changed paths: A /branches/prog/bam/misc/all2sam.pl (from /branches/prog/bam/misc/all2tam.pl:649) D /branches/prog/bam/misc/all2tam.pl A /branches/prog/bam/misc/maq2sam.c (from /branches/prog/bam/misc/maq2tam.c:699) D /branches/prog/bam/misc/maq2tam.c rename tam to sam ------------------------------------------------------------------------ r699 | lh3 | 2008-11-25 13:14:49 +0000 (Tue, 25 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/misc/maq2tam.c change for the new specification ------------------------------------------------------------------------ r698 | lh3 | 2008-11-24 13:15:20 +0000 (Mon, 24 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/bam.h M /branches/prog/bam/razf.c M /branches/prog/bam/razf.h * add a fake BGZF mode to razf. It is fake in that it loads razf index into memory but gives BGZF like virtual offset ------------------------------------------------------------------------ r697 | lh3 | 2008-11-24 09:53:44 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: A /branches/prog/bam/ChangeLog change log ------------------------------------------------------------------------ r696 | lh3 | 2008-11-24 09:53:23 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/bgzf.c updated bgzf, on behalf of Bob ------------------------------------------------------------------------ r695 | lh3 | 2008-11-23 11:40:31 +0000 (Sun, 23 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/bam_index.c M /branches/prog/bam/razf.c fixed a bug in razf ------------------------------------------------------------------------ r694 | lh3 | 2008-11-22 16:23:52 +0000 (Sat, 22 Nov 2008) | 4 lines Changed paths: M /branches/prog/bam/bam_index.c M /branches/prog/bam/bam_lpileup.c M /branches/prog/bam/bam_tview.c M /branches/prog/bam/bamtk.c * bam-0.1.0-40 * fixed two small memory leaks * fixed a memory problem when seek outside the length of the sequence ------------------------------------------------------------------------ r693 | lh3 | 2008-11-22 16:10:04 +0000 (Sat, 22 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/bam_index.c M /branches/prog/bam/bamtk.c * bam-0.1.0-39 * fixed an uninitialized warning. This does not matter in fact ------------------------------------------------------------------------ r692 | lh3 | 2008-11-22 15:44:05 +0000 (Sat, 22 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/razf.c M /branches/prog/bam/razf.h Jue's new razf ------------------------------------------------------------------------ r691 | lh3 | 2008-11-21 21:30:39 +0000 (Fri, 21 Nov 2008) | 4 lines Changed paths: M /branches/prog/bam/Makefile M /branches/prog/bam/bam.h M /branches/prog/bam/bam_index.c M /branches/prog/bam/bamtk.c M /branches/prog/bam/bgzip.c * bam-0.1.0-38 * get rid of some warings in bgzip.c * potentially improve performance in indexing for BGZF ------------------------------------------------------------------------ r690 | lh3 | 2008-11-21 21:15:51 +0000 (Fri, 21 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/bgzf.c I think I have fixed the bug in bgzf ------------------------------------------------------------------------ r689 | lh3 | 2008-11-21 20:48:56 +0000 (Fri, 21 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/bgzf.c bug fix by Bob ------------------------------------------------------------------------ r688 | lh3 | 2008-11-21 20:37:27 +0000 (Fri, 21 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/bam.h M /branches/prog/bam/bam_index.c fixed a bug due to the name change in _IOLIB ------------------------------------------------------------------------ r687 | lh3 | 2008-11-21 14:42:56 +0000 (Fri, 21 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/bgzf.c fix small things ------------------------------------------------------------------------ r686 | lh3 | 2008-11-21 14:37:59 +0000 (Fri, 21 Nov 2008) | 2 lines Changed paths: A /branches/prog/bam/bgzf.c A /branches/prog/bam/bgzf.h A /branches/prog/bam/bgzip.c Bob's BGZF format, although currently buggy ------------------------------------------------------------------------ r685 | lh3 | 2008-11-21 09:48:20 +0000 (Fri, 21 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/bam_index.c M /branches/prog/bam/bam_tview.c M /branches/prog/bam/bamtk.c * bam-0.1.0-37 * improve interface a little bit ------------------------------------------------------------------------ r684 | lh3 | 2008-11-21 09:30:18 +0000 (Fri, 21 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/bam_tview.c M /branches/prog/bam/bamtk.c * bam-0.1.0-36 * improve the interface of tview, a little bit ------------------------------------------------------------------------ r683 | lh3 | 2008-11-20 22:33:54 +0000 (Thu, 20 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/bam_tview.c a little better viewer ------------------------------------------------------------------------ r682 | lh3 | 2008-11-20 22:27:01 +0000 (Thu, 20 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/bam.h M /branches/prog/bam/bam_tview.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-35 * better viewer ------------------------------------------------------------------------ r681 | lh3 | 2008-11-20 20:51:16 +0000 (Thu, 20 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/Makefile M /branches/prog/bam/bam_tview.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-34 * tview is now a component of bamtk ------------------------------------------------------------------------ r680 | lh3 | 2008-11-20 19:17:30 +0000 (Thu, 20 Nov 2008) | 2 lines Changed paths: A /branches/prog/bam/bam_tview.c text alignment viewer ------------------------------------------------------------------------ r679 | lh3 | 2008-11-20 19:17:15 +0000 (Thu, 20 Nov 2008) | 5 lines Changed paths: M /branches/prog/bam/Makefile M /branches/prog/bam/bam.h M /branches/prog/bam/bam_index.c M /branches/prog/bam/bam_lpileup.c M /branches/prog/bam/bam_pileup.c M /branches/prog/bam/bamtk.1 M /branches/prog/bam/bamtk.c M /branches/prog/bam/faidx.c * bamtk-0.1.0-33 * added routines to reset pileup bufferes * fixed a bug in faidx * add text alignment viewer ------------------------------------------------------------------------ r678 | lh3 | 2008-11-20 11:05:02 +0000 (Thu, 20 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/Makefile A /branches/prog/bam/bam_lpileup.c (from /branches/prog/bam/bam_tview.c:668) D /branches/prog/bam/bam_tview.c rename tview as lpileup ------------------------------------------------------------------------ r677 | lh3 | 2008-11-20 10:08:52 +0000 (Thu, 20 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/razf.c fixed a bug in razf ------------------------------------------------------------------------ r676 | lh3 | 2008-11-19 22:52:20 +0000 (Wed, 19 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/bam.h M /branches/prog/bam/bam_index.c M /branches/prog/bam/faidx.h add documentations ------------------------------------------------------------------------ r674 | lh3 | 2008-11-19 21:39:17 +0000 (Wed, 19 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/bam.h M /branches/prog/bam/bamtk.1 M /branches/prog/bam/faidx.h update documentation ------------------------------------------------------------------------ r673 | lh3 | 2008-11-19 21:19:03 +0000 (Wed, 19 Nov 2008) | 2 lines Changed paths: A /branches/prog/bam/bamtk.1 add manual page ------------------------------------------------------------------------ r672 | lh3 | 2008-11-19 16:40:49 +0000 (Wed, 19 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/bamtk.c M /branches/prog/bam/faidx.c * bamtk-0.1.0-32 * make faidx more error resistant ------------------------------------------------------------------------ r671 | lh3 | 2008-11-19 16:09:55 +0000 (Wed, 19 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/faidx.h add index ------------------------------------------------------------------------ r670 | lh3 | 2008-11-19 16:02:39 +0000 (Wed, 19 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/bam_pileup.c M /branches/prog/bam/bamtk.c M /branches/prog/bam/faidx.c * bamtk-0.1.0-31 * show reference sequence in pileup -v (not in the default pileup) ------------------------------------------------------------------------ r669 | lh3 | 2008-11-19 14:51:17 +0000 (Wed, 19 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/Makefile M /branches/prog/bam/bamtk.c M /branches/prog/bam/faidx.c * bamtk-0.1.0-30 * put faidx in bamtk and remove faidx_main.c ------------------------------------------------------------------------ r668 | lh3 | 2008-11-19 14:15:05 +0000 (Wed, 19 Nov 2008) | 4 lines Changed paths: M /branches/prog/bam/Makefile M /branches/prog/bam/bam_index.c M /branches/prog/bam/bam_tview.c M /branches/prog/bam/bamtk.c A /branches/prog/bam/faidx.c A /branches/prog/bam/faidx.h M /branches/prog/bam/razf.c * bamtk-0.1.0-29 * fixed a bug in tview.c * prepare to add faidx ------------------------------------------------------------------------ r667 | lh3 | 2008-11-19 10:20:45 +0000 (Wed, 19 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/bam.h M /branches/prog/bam/razf.c M /branches/prog/bam/razf.h gzip-compatible razf ------------------------------------------------------------------------ r664 | lh3 | 2008-11-18 12:50:23 +0000 (Tue, 18 Nov 2008) | 5 lines Changed paths: M /branches/prog/bam/bam.h M /branches/prog/bam/bam_index.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-28 * fetch: fixed a bug at an array boundary * fetch: fixed a bug when the whole chromosome is retrieved * add linear index ------------------------------------------------------------------------ r663 | lh3 | 2008-11-17 21:29:22 +0000 (Mon, 17 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/Makefile M /branches/prog/bam/bam.c M /branches/prog/bam/bam.h M /branches/prog/bam/bam_import.c M /branches/prog/bam/bam_pileup.c M /branches/prog/bam/bam_tview.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-27 * put l_qseq into core and move l_aux to bam1_t ------------------------------------------------------------------------ r662 | lh3 | 2008-11-17 20:55:16 +0000 (Mon, 17 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/bam.c M /branches/prog/bam/bam.h M /branches/prog/bam/bam_import.c M /branches/prog/bam/bam_index.c M /branches/prog/bam/bam_pileup.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-26 * save seq and qual separately ------------------------------------------------------------------------ r661 | lh3 | 2008-11-17 13:09:37 +0000 (Mon, 17 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/bam.h little ------------------------------------------------------------------------ r660 | lh3 | 2008-11-17 13:06:14 +0000 (Mon, 17 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/bam.h more documentations ------------------------------------------------------------------------ r659 | lh3 | 2008-11-17 12:55:08 +0000 (Mon, 17 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/bam_pileup.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-25 * make tview work for TAM ------------------------------------------------------------------------ r658 | lh3 | 2008-11-17 12:50:21 +0000 (Mon, 17 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/Makefile M /branches/prog/bam/bam.h M /branches/prog/bam/bam_pileup.c M /branches/prog/bam/bam_tview.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-24 * make tview as an independent module ------------------------------------------------------------------------ r657 | lh3 | 2008-11-17 11:26:06 +0000 (Mon, 17 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/Makefile M /branches/prog/bam/bam.h M /branches/prog/bam/bam_pileup.c change little ------------------------------------------------------------------------ r656 | lh3 | 2008-11-16 21:33:19 +0000 (Sun, 16 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/bam_pileup.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-23 * also add tview for TAM ------------------------------------------------------------------------ r655 | lh3 | 2008-11-16 21:29:46 +0000 (Sun, 16 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/Makefile M /branches/prog/bam/bam_tview.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-22 * make tview more efficient for deep depth ------------------------------------------------------------------------ r654 | lh3 | 2008-11-16 20:52:19 +0000 (Sun, 16 Nov 2008) | 4 lines Changed paths: M /branches/prog/bam/Makefile M /branches/prog/bam/bam_import.c M /branches/prog/bam/bam_pileup.c A /branches/prog/bam/bam_tview.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-21 * fixed bug in the TAM parser: lowercase not recognized * unfinished function to leveled pileup (tview) ------------------------------------------------------------------------ r653 | lh3 | 2008-11-15 12:58:36 +0000 (Sat, 15 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/bam.h M /branches/prog/bam/bam_pileup.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-20 * pileup now display deleted bases as '*' ------------------------------------------------------------------------ r652 | lh3 | 2008-11-15 09:58:39 +0000 (Sat, 15 Nov 2008) | 4 lines Changed paths: M /branches/prog/bam/bam_index.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-19 * fixed a bug in fetch() * reduce memory in indexing ------------------------------------------------------------------------ r651 | lh3 | 2008-11-14 21:56:05 +0000 (Fri, 14 Nov 2008) | 5 lines Changed paths: M /branches/prog/bam/Makefile M /branches/prog/bam/bam.h M /branches/prog/bam/bam_index.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-18 * important changes are made to index: the index size is increased, but now we have no limit on file sizes and the new method potentially works with BGZF, Bob's new compression format. ------------------------------------------------------------------------ r650 | lh3 | 2008-11-14 16:03:22 +0000 (Fri, 14 Nov 2008) | 4 lines Changed paths: M /branches/prog/bam/bam.h M /branches/prog/bam/bam_index.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-17 * more comments in bam.h * fixed a bug in bam_index.c ------------------------------------------------------------------------ r649 | lh3 | 2008-11-13 16:04:18 +0000 (Thu, 13 Nov 2008) | 4 lines Changed paths: M /branches/prog/bam/bam.c M /branches/prog/bam/bam.h M /branches/prog/bam/bam_import.c M /branches/prog/bam/bam_index.c M /branches/prog/bam/bam_pileup.c M /branches/prog/bam/bam_sort.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-16 * use macros to retrieve pointers from bam1_t and thus reduce the size of bam1_t struct. ------------------------------------------------------------------------ r648 | lh3 | 2008-11-13 13:21:39 +0000 (Thu, 13 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/bam_sort.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-15 * make more things work over pipe ------------------------------------------------------------------------ r647 | lh3 | 2008-11-13 12:49:28 +0000 (Thu, 13 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/misc/maq2tam.c fixed a bug in maq2tam ------------------------------------------------------------------------ r646 | lh3 | 2008-11-13 11:46:59 +0000 (Thu, 13 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/Makefile M /branches/prog/bam/misc/Makefile M /branches/prog/bam/misc/maq2tam.c * bug fix in maq2tam.c * improve Makefile ------------------------------------------------------------------------ r645 | lh3 | 2008-11-13 11:39:46 +0000 (Thu, 13 Nov 2008) | 3 lines Changed paths: A /branches/prog/bam/misc/Makefile M /branches/prog/bam/misc/maq2tam.c * corrected maq2tam * add Makefile ------------------------------------------------------------------------ r644 | lh3 | 2008-11-13 11:25:45 +0000 (Thu, 13 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/razf.c fixed the bug in buffered write (on behalf of Jue) ------------------------------------------------------------------------ r643 | lh3 | 2008-11-13 10:53:42 +0000 (Thu, 13 Nov 2008) | 2 lines Changed paths: D /branches/prog/bam/all2tam.pl A /branches/prog/bam/misc/all2tam.pl (from /branches/prog/bam/all2tam.pl:642) move to misc ------------------------------------------------------------------------ r642 | lh3 | 2008-11-13 10:53:23 +0000 (Thu, 13 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/all2tam.pl change tag ------------------------------------------------------------------------ r641 | lh3 | 2008-11-13 10:53:12 +0000 (Thu, 13 Nov 2008) | 2 lines Changed paths: D /branches/prog/bam/utils has been renamed ------------------------------------------------------------------------ r640 | lh3 | 2008-11-13 10:52:50 +0000 (Thu, 13 Nov 2008) | 2 lines Changed paths: A /branches/prog/bam/misc (from /branches/prog/bam/utils:639) rename ------------------------------------------------------------------------ r639 | lh3 | 2008-11-13 10:52:35 +0000 (Thu, 13 Nov 2008) | 2 lines Changed paths: A /branches/prog/bam/utils A /branches/prog/bam/utils/maq2tam.c utilities (converters and so on) ------------------------------------------------------------------------ r638 | lh3 | 2008-11-12 22:24:22 +0000 (Wed, 12 Nov 2008) | 4 lines Changed paths: M /branches/prog/bam/bam.c M /branches/prog/bam/bam.h M /branches/prog/bam/bam_import.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-14 * copy the text header to BAM * add BAM1 header flag ------------------------------------------------------------------------ r637 | lh3 | 2008-11-12 14:56:08 +0000 (Wed, 12 Nov 2008) | 4 lines Changed paths: M /branches/prog/bam/bam.h M /branches/prog/bam/bam_index.c M /branches/prog/bam/bamtk.c M /branches/prog/bam/razf.c * bamtk-0.1.0-13 * fixed a bug in razf * improved and fixed potential bugs in index ------------------------------------------------------------------------ r636 | lh3 | 2008-11-12 11:57:13 +0000 (Wed, 12 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/bam.h M /branches/prog/bam/bam_index.c M /branches/prog/bam/bam_pileup.c M /branches/prog/bam/bamtk.c update documentation in the HeaderDOC format ------------------------------------------------------------------------ r635 | lh3 | 2008-11-12 10:08:38 +0000 (Wed, 12 Nov 2008) | 4 lines Changed paths: M /branches/prog/bam/bam.c M /branches/prog/bam/bam.h M /branches/prog/bam/bam_import.c M /branches/prog/bam/bam_index.c M /branches/prog/bam/bam_pileup.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-12 * more documentations * rename baf1_core_t as bam1_core_t ------------------------------------------------------------------------ r634 | lh3 | 2008-11-11 23:00:35 +0000 (Tue, 11 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/bam.h M /branches/prog/bam/bam_pileup.c documentation ------------------------------------------------------------------------ r633 | lh3 | 2008-11-11 21:23:49 +0000 (Tue, 11 Nov 2008) | 4 lines Changed paths: M /branches/prog/bam/bam_index.c M /branches/prog/bam/bam_pileup.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-11 * give up regional pileup. We can now use pipe to mimic that. * for index file, change suffix .idx to .bmi ------------------------------------------------------------------------ r632 | lh3 | 2008-11-11 21:00:11 +0000 (Tue, 11 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/bam.h M /branches/prog/bam/bam_import.c M /branches/prog/bam/bam_pileup.c M /branches/prog/bam/bamtk.c M /branches/prog/bam/razf.c * bamtk-0.1.0-10 * make pileup work on TAM ------------------------------------------------------------------------ r631 | lh3 | 2008-11-11 09:20:29 +0000 (Tue, 11 Nov 2008) | 4 lines Changed paths: M /branches/prog/bam/bam_pileup.c M /branches/prog/bam/bamtk.c M /branches/prog/bam/razf.c M /branches/prog/bam/razf.h M /branches/prog/bam/razip.c * bamtk-0.1.0-9 * razf now supports streaming * prepare to improve pileup (have not yet) ------------------------------------------------------------------------ r630 | lh3 | 2008-11-10 18:34:40 +0000 (Mon, 10 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/bam.h M /branches/prog/bam/bam_import.c M /branches/prog/bam/bam_pileup.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-8 * improve the interface of TAM parser ------------------------------------------------------------------------ r629 | lh3 | 2008-11-10 13:06:13 +0000 (Mon, 10 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/bam_pileup.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-7 * almost nothing ------------------------------------------------------------------------ r628 | lh3 | 2008-11-10 12:56:36 +0000 (Mon, 10 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/bam.c M /branches/prog/bam/bam.h M /branches/prog/bam/bam_pileup.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-6 * fixed a bug in bam_pileup.c ------------------------------------------------------------------------ r627 | lh3 | 2008-11-10 11:32:46 +0000 (Mon, 10 Nov 2008) | 4 lines Changed paths: M /branches/prog/bam/bam.h M /branches/prog/bam/bam_pileup.c M /branches/prog/bam/bamtk.c M /branches/prog/bam/razf.c * bamtk-0.1.0-5 * fixed a bug in razf.c, caused by my modifications * improve the interface of pileup. Now it will be slower but more flexible ------------------------------------------------------------------------ r626 | lh3 | 2008-11-09 20:51:04 +0000 (Sun, 09 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/bam.h M /branches/prog/bam/bamtk.c * bamtk-0.1.0-4 * view: dumping binary output ------------------------------------------------------------------------ r625 | lh3 | 2008-11-09 20:31:54 +0000 (Sun, 09 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/bam.c M /branches/prog/bam/bam.h M /branches/prog/bam/bam_import.c M /branches/prog/bam/bam_index.c M /branches/prog/bam/bam_pileup.c M /branches/prog/bam/bam_sort.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-3 * rename functions ------------------------------------------------------------------------ r624 | lh3 | 2008-11-09 15:07:32 +0000 (Sun, 09 Nov 2008) | 2 lines Changed paths: M /branches/prog/bam/bam.h add comments ------------------------------------------------------------------------ r623 | lh3 | 2008-11-08 22:32:49 +0000 (Sat, 08 Nov 2008) | 4 lines Changed paths: M /branches/prog/bam/bam_index.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-2 * improve indexing for a mixture of long and short reads, although currently I do not know whether it really works... ------------------------------------------------------------------------ r622 | lh3 | 2008-11-08 22:13:58 +0000 (Sat, 08 Nov 2008) | 3 lines Changed paths: M /branches/prog/bam/bam_index.c M /branches/prog/bam/bamtk.c * bamtk-0.1.0-1 * prepare for improving indexing algorithm ------------------------------------------------------------------------ r621 | lh3 | 2008-11-08 20:28:09 +0000 (Sat, 08 Nov 2008) | 4 lines Changed paths: A /branches/prog/bam/all2tam.pl M /branches/prog/bam/bam.c M /branches/prog/bam/bam.h M /branches/prog/bam/bam_import.c M /branches/prog/bam/bamtk.c D /branches/prog/bam/tam_utils.pl * bamtk-0.1.0 * smarter integers * rename tam_utils.pl to all2tam.pl ------------------------------------------------------------------------ r620 | lh3 | 2008-11-08 17:17:22 +0000 (Sat, 08 Nov 2008) | 2 lines Changed paths: A /branches/prog/bam A /branches/prog/bam/Makefile A /branches/prog/bam/bam.c A /branches/prog/bam/bam.h A /branches/prog/bam/bam_endian.h A /branches/prog/bam/bam_import.c A /branches/prog/bam/bam_index.c A /branches/prog/bam/bam_pileup.c A /branches/prog/bam/bam_sort.c A /branches/prog/bam/bamtk.c A /branches/prog/bam/khash.h A /branches/prog/bam/ksort.h A /branches/prog/bam/kstream.h A /branches/prog/bam/razf.c A /branches/prog/bam/razf.h A /branches/prog/bam/razip.c A /branches/prog/bam/tam_utils.pl A /branches/prog/bam/zutil.h The Binary Alignment/Mapping format. ------------------------------------------------------------------------