------------------------------------------------------------------------ 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) ------------------------------------------------------------------------