------------------------------------------------------------------------ r244 | lh3lh3 | 2009-04-25 11:49:40 +0100 (Sat, 25 Apr 2009) | 3 lines Changed paths: M /trunk/samtools/bam_md.c M /trunk/samtools/bamtk.c * samtools-0.1.3-6 (r244) * fixed segfault for unmapped reads ------------------------------------------------------------------------ r243 | lh3lh3 | 2009-04-24 21:27:26 +0100 (Fri, 24 Apr 2009) | 5 lines Changed paths: M /trunk/samtools/bam.h M /trunk/samtools/bam_maqcns.c M /trunk/samtools/bam_md.c M /trunk/samtools/bamtk.c * samtools-0.1.3-5 (r243) * fixed a long existing bug which may cause memory leak * check MD * consensus calling now works with "=", but indel calling not ------------------------------------------------------------------------ r242 | lh3lh3 | 2009-04-24 20:44:46 +0100 (Fri, 24 Apr 2009) | 3 lines Changed paths: M /trunk/samtools/bam_md.c M /trunk/samtools/bamtk.c * samtools-0.1.3-4 (r242) * fixed a memory leak ------------------------------------------------------------------------ r240 | lh3lh3 | 2009-04-24 16:40:18 +0100 (Fri, 24 Apr 2009) | 5 lines Changed paths: M /trunk/samtools/Makefile M /trunk/samtools/Makefile.lite M /trunk/samtools/bam.h M /trunk/samtools/bam_aux.c A /trunk/samtools/bam_md.c M /trunk/samtools/bam_plcmd.c M /trunk/samtools/bamtk.c * samtools-0.1.3-3 (r240) * generate MD tag * generate "=" bases * the plain pileup now support "=" bases, but consensus calling and glfgen may fail ------------------------------------------------------------------------ r239 | lh3lh3 | 2009-04-24 12:08:20 +0100 (Fri, 24 Apr 2009) | 5 lines Changed paths: M /trunk/samtools/bam.h M /trunk/samtools/bam_aux.c M /trunk/samtools/bamtk.c * samtools-0.1.3-2 (r239) * fixed bugs in bam_aux.c (these functions nevered used by samtools) * removed bam_aux_init()/bam_aux_destroy() * added tagview for testing bam_aux ------------------------------------------------------------------------ r235 | lh3lh3 | 2009-04-21 23:17:39 +0100 (Tue, 21 Apr 2009) | 3 lines Changed paths: M /trunk/samtools/bam_pileup.c M /trunk/samtools/bamtk.c * samtools-0.1.3-1 * fixed a bug in pileup: the first read in a chromosome may not be printed ------------------------------------------------------------------------ r232 | lh3lh3 | 2009-04-16 15:25:43 +0100 (Thu, 16 Apr 2009) | 2 lines Changed paths: M /trunk/samtools/Makefile.lite a missing file in Makefile.lite ------------------------------------------------------------------------ r227 | lh3lh3 | 2009-04-15 22:02:53 +0100 (Wed, 15 Apr 2009) | 2 lines Changed paths: M /trunk/samtools/NEWS M /trunk/samtools/bamtk.c Release samtools-0.1.3 ------------------------------------------------------------------------ r223 | lh3lh3 | 2009-04-15 14:31:32 +0100 (Wed, 15 Apr 2009) | 3 lines Changed paths: M /trunk/samtools/bam_plcmd.c M /trunk/samtools/bamtk.c * samtools-0.1.2-28 * make samtools more robust to weird input such as empty file ------------------------------------------------------------------------ r222 | lh3lh3 | 2009-04-15 14:05:33 +0100 (Wed, 15 Apr 2009) | 2 lines Changed paths: M /trunk/samtools/ChangeLog M /trunk/samtools/NEWS M /trunk/samtools/samtools.1 prepare for release 0.1.3 ------------------------------------------------------------------------ r221 | lh3lh3 | 2009-04-15 13:32:14 +0100 (Wed, 15 Apr 2009) | 2 lines Changed paths: A /trunk/samtools/misc/blast2sam.pl convert NCBI-BLASTN to SAM ------------------------------------------------------------------------ r220 | lh3lh3 | 2009-04-15 13:18:19 +0100 (Wed, 15 Apr 2009) | 3 lines Changed paths: M /trunk/samtools/bam_lpileup.c M /trunk/samtools/bamtk.c * samtools-0.1.2-27 * fixed a small memory leak in tview ------------------------------------------------------------------------ r219 | lh3lh3 | 2009-04-15 13:00:08 +0100 (Wed, 15 Apr 2009) | 3 lines Changed paths: M /trunk/samtools/bam_rmdup.c M /trunk/samtools/bamtk.c * samtools-0.1.2-26 * fixed a bug in rmdup when there are unmapped reads ------------------------------------------------------------------------ r218 | lh3lh3 | 2009-04-14 22:28:58 +0100 (Tue, 14 Apr 2009) | 2 lines Changed paths: M /trunk/samtools/ChangeLog M /trunk/samtools/NEWS proposed NEWS for the new release (have not yet) ------------------------------------------------------------------------ r216 | lh3lh3 | 2009-04-14 22:10:46 +0100 (Tue, 14 Apr 2009) | 4 lines Changed paths: M /trunk/samtools/misc/samtools.pl * samtools.pl-0.1.1 * improve indelFilter to avoid filtering true indels. The new filter relies on the new pileup indel line implemented in samtools-0.1.2-25 ------------------------------------------------------------------------ r215 | lh3lh3 | 2009-04-14 22:04:19 +0100 (Tue, 14 Apr 2009) | 4 lines Changed paths: M /trunk/samtools/bam_maqcns.c M /trunk/samtools/bam_plcmd.c M /trunk/samtools/bamtk.c M /trunk/samtools/samtools.1 * samtools-0.1.2-25 * change the pileup indel line to shows the number of alignments actually containing indels ------------------------------------------------------------------------ r211 | lh3lh3 | 2009-04-13 12:07:13 +0100 (Mon, 13 Apr 2009) | 2 lines Changed paths: M /trunk/samtools/ChangeLog update ChangeLog from "svn log" ------------------------------------------------------------------------ r210 | lh3lh3 | 2009-04-12 20:57:05 +0100 (Sun, 12 Apr 2009) | 4 lines Changed paths: M /trunk/samtools/bam.c M /trunk/samtools/bam_import.c M /trunk/samtools/bam_sort.c M /trunk/samtools/bamtk.c M /trunk/samtools/kseq.h * samtools-0.1.2-24 * in merge, gives a warning rather than error if the target sequence length is different * allow empty header ------------------------------------------------------------------------ r209 | lh3lh3 | 2009-04-12 20:32:44 +0100 (Sun, 12 Apr 2009) | 3 lines Changed paths: M /trunk/samtools/bam.c M /trunk/samtools/bam_import.c M /trunk/samtools/bamtk.c * samtools-0.1.2-23 * recognize '*' at the QUAL field ------------------------------------------------------------------------ r208 | lh3lh3 | 2009-04-12 20:08:02 +0100 (Sun, 12 Apr 2009) | 3 lines Changed paths: M /trunk/samtools/bam_import.c M /trunk/samtools/bamtk.c M /trunk/samtools/kseq.h * samtools-0.1.2-22 * the field separater is TAB only, now ------------------------------------------------------------------------ r207 | lh3lh3 | 2009-04-08 15:18:03 +0100 (Wed, 08 Apr 2009) | 2 lines Changed paths: M /trunk/samtools/examples/ex1.sam.gz * fixed the problem in the example alignment due to the bug in fixmate ------------------------------------------------------------------------ r206 | lh3lh3 | 2009-04-08 15:15:05 +0100 (Wed, 08 Apr 2009) | 3 lines Changed paths: M /trunk/samtools/bam_mate.c M /trunk/samtools/bamtk.c M /trunk/samtools/misc/soap2sam.pl * samtools-0.1.2-21 * fixed a nasty bug in `fixmate' ------------------------------------------------------------------------ r205 | lh3lh3 | 2009-04-08 10:57:08 +0100 (Wed, 08 Apr 2009) | 2 lines Changed paths: M /trunk/samtools/misc/bowtie2sam.pl M /trunk/samtools/misc/soap2sam.pl M /trunk/samtools/misc/wgsim_eval.pl make the script robust to the bugs in SOAP-2.1.7 ------------------------------------------------------------------------ r200 | lh3lh3 | 2009-04-02 15:14:56 +0100 (Thu, 02 Apr 2009) | 3 lines Changed paths: M /trunk/samtools/bam_stat.c M /trunk/samtools/bamtk.c * samtools-0.1.2-20 * check if file is truncated in flagstat ------------------------------------------------------------------------ r199 | lh3lh3 | 2009-04-02 15:09:10 +0100 (Thu, 02 Apr 2009) | 3 lines Changed paths: M /trunk/samtools/bamtk.c * samtools-0.1.2-19 * print the header if requested ------------------------------------------------------------------------ r193 | lh3lh3 | 2009-03-27 15:09:50 +0000 (Fri, 27 Mar 2009) | 3 lines Changed paths: M /trunk/samtools/bam_plcmd.c M /trunk/samtools/bamtk.c * samtools-0.1.2-18 * fixed a minor bug reported by Nils Homer ------------------------------------------------------------------------ r185 | lh3lh3 | 2009-03-24 11:50:32 +0000 (Tue, 24 Mar 2009) | 2 lines Changed paths: A /trunk/samtools/Makefile (from /trunk/samtools/Makefile.std:184) D /trunk/samtools/Makefile.std A /trunk/samtools/misc/Makefile (from /trunk/samtools/misc/Makefile.std:184) D /trunk/samtools/misc/Makefile.std rename Makefile.std as Makefile. GNU building systerm is not ready and may take some time... ------------------------------------------------------------------------ r184 | lh3lh3 | 2009-03-24 10:36:38 +0000 (Tue, 24 Mar 2009) | 4 lines Changed paths: D /trunk/samtools/Makefile A /trunk/samtools/Makefile.std (from /trunk/samtools/Makefile:183) M /trunk/samtools/bam_sort.c M /trunk/samtools/bam_tview.c M /trunk/samtools/bamtk.c D /trunk/samtools/misc/Makefile A /trunk/samtools/misc/Makefile.std (from /trunk/samtools/misc/Makefile:182) M /trunk/samtools/samtools.1 * samtools-0.1.2-17 * incorporating Nils' changes * rename Makefile to Makefile.std and prepare to add the GNU building systerms (also by Nils) ------------------------------------------------------------------------ r183 | lh3lh3 | 2009-03-24 10:30:23 +0000 (Tue, 24 Mar 2009) | 4 lines Changed paths: M /trunk/samtools/Makefile M /trunk/samtools/bam_import.c M /trunk/samtools/bam_maqcns.c M /trunk/samtools/bam_maqcns.h M /trunk/samtools/bam_plcmd.c M /trunk/samtools/bamtk.c M /trunk/samtools/kseq.h A /trunk/samtools/kstring.c A /trunk/samtools/kstring.h * samtools-0.1.2-16 * made pileup take a list of proposed indels. An insertion is N at the moment. * added my kstring library for a bit complex parsing of the position list. ------------------------------------------------------------------------ r169 | lh3lh3 | 2009-03-12 13:40:14 +0000 (Thu, 12 Mar 2009) | 3 lines Changed paths: M /trunk/samtools/misc/soap2sam.pl * soap2sam.pl-0.1.2 * more robust to truncated soap output ------------------------------------------------------------------------ r168 | lh3lh3 | 2009-03-11 10:49:00 +0000 (Wed, 11 Mar 2009) | 2 lines Changed paths: M /trunk/samtools/Makefile.lite added bam_stat.o to Makefile.lite ------------------------------------------------------------------------ r167 | lh3lh3 | 2009-03-10 22:11:31 +0000 (Tue, 10 Mar 2009) | 3 lines Changed paths: M /trunk/samtools/bam_maqcns.c M /trunk/samtools/bamtk.c * samtools-0.1.2-15 * generate RMS of mapQ instead of max mapQ ------------------------------------------------------------------------ r166 | lh3lh3 | 2009-03-10 22:06:45 +0000 (Tue, 10 Mar 2009) | 3 lines Changed paths: M /trunk/samtools/bam_plcmd.c M /trunk/samtools/bamtk.c M /trunk/samtools/glf.c M /trunk/samtools/glf.h M /trunk/samtools/misc/Makefile * samtools-0.1.2-14 * implemented GLFv3 ------------------------------------------------------------------------ r159 | lh3lh3 | 2009-03-03 11:26:08 +0000 (Tue, 03 Mar 2009) | 3 lines Changed paths: M /trunk/samtools/bam_plcmd.c M /trunk/samtools/bamtk.c * samtools-0.1.2-13 * fixed a minor bug in displaying pileup ------------------------------------------------------------------------ r158 | lh3lh3 | 2009-03-03 11:24:16 +0000 (Tue, 03 Mar 2009) | 3 lines Changed paths: M /trunk/samtools/ChangeLog M /trunk/samtools/bamtk.c * samtools-0.1.2-12 * optionally print SAM header ------------------------------------------------------------------------ r153 | lh3lh3 | 2009-03-02 10:45:28 +0000 (Mon, 02 Mar 2009) | 3 lines Changed paths: M /trunk/samtools/bamtk.c M /trunk/samtools/glf.c * samtools-0.1.2-11 * use "GLF\3" as the magic for GLFv3 files ------------------------------------------------------------------------ r152 | lh3lh3 | 2009-03-02 10:39:09 +0000 (Mon, 02 Mar 2009) | 5 lines Changed paths: M /trunk/samtools/Makefile M /trunk/samtools/bam_import.c M /trunk/samtools/bam_index.c M /trunk/samtools/bam_plcmd.c M /trunk/samtools/bamtk.c M /trunk/samtools/glf.c M /trunk/samtools/glf.h * samtools-0.1.2-10 * fixed a bug in import: core.bin is undefined for unmapped reads * this bug can be alleviated (not completely solved) in bam_index.c * update to GLFv3: pos is changed to offset for better compression ------------------------------------------------------------------------ r151 | lh3lh3 | 2009-03-01 15:18:43 +0000 (Sun, 01 Mar 2009) | 3 lines Changed paths: M /trunk/samtools/misc/wgsim.c * wgsim-0.2.3 * fixed a bug in simulating indels ------------------------------------------------------------------------ r145 | lh3lh3 | 2009-02-26 19:43:57 +0000 (Thu, 26 Feb 2009) | 4 lines Changed paths: M /trunk/samtools/misc/wgsim.c * wgsim-0.2.2 * allow to print mismatch information as fastq comment. MAQ does not like long read names. ------------------------------------------------------------------------ r141 | lh3lh3 | 2009-02-26 14:53:03 +0000 (Thu, 26 Feb 2009) | 6 lines Changed paths: M /trunk/samtools/ChangeLog M /trunk/samtools/misc/wgsim.c M /trunk/samtools/misc/wgsim_eval.pl * wgsim-0.2.1 * fixed a bug about color read coordinates * fixed a bug in read names * wgsim_eval.pl-0.1.3 * make the script work with color reads ------------------------------------------------------------------------ r140 | lh3lh3 | 2009-02-26 14:02:57 +0000 (Thu, 26 Feb 2009) | 2 lines Changed paths: M /trunk/samtools/misc/Makefile M /trunk/samtools/misc/wgsim.c * wgsim: added a note ------------------------------------------------------------------------ r139 | lh3lh3 | 2009-02-26 11:39:08 +0000 (Thu, 26 Feb 2009) | 7 lines Changed paths: M /trunk/samtools/misc/wgsim.c M /trunk/samtools/misc/wgsim_eval.pl * wgsim-0.2.0 * considerable code clean up * print number of substitutions/indels/errors on each read * potentially support SOLiD simulation, though not tested at the moment * wgsim_eval.pl-0.1.2 * change in accordant with wgsim ------------------------------------------------------------------------ r129 | lh3lh3 | 2009-02-18 22:23:27 +0000 (Wed, 18 Feb 2009) | 3 lines Changed paths: M /trunk/samtools/bam_index.c M /trunk/samtools/bamtk.c * samtools-0.1.2-9 * fixed a bug in bam_fetch, caused by completely contained adjacent chunks ------------------------------------------------------------------------ r128 | bhandsaker | 2009-02-18 19:06:57 +0000 (Wed, 18 Feb 2009) | 2 lines Changed paths: M /trunk/samtools/bamtk.c Fix annoying segv when invalid region specified. ------------------------------------------------------------------------ r127 | lh3lh3 | 2009-02-17 10:49:55 +0000 (Tue, 17 Feb 2009) | 2 lines Changed paths: D /trunk/samtools/misc/indel_filter.pl A /trunk/samtools/misc/samtools.pl * move indel_filter.pl to samtools.pl ------------------------------------------------------------------------ r126 | lh3lh3 | 2009-02-14 21:22:30 +0000 (Sat, 14 Feb 2009) | 3 lines Changed paths: M /trunk/samtools/bam_mate.c M /trunk/samtools/bamtk.c * samtools-0.1.2-7 * fixed a bug in fixmate: SE reads are flagged as BAM_FMUNMAP ------------------------------------------------------------------------ r125 | lh3lh3 | 2009-02-13 09:54:45 +0000 (Fri, 13 Feb 2009) | 3 lines Changed paths: M /trunk/samtools/bam_stat.c M /trunk/samtools/bamtk.c * samtools-0.1.2-7 * fixed a minor bug in flagstat ------------------------------------------------------------------------ r124 | lh3lh3 | 2009-02-12 11:15:32 +0000 (Thu, 12 Feb 2009) | 3 lines Changed paths: M /trunk/samtools/bam_maqcns.c M /trunk/samtools/bamtk.c M /trunk/samtools/misc/indel_filter.pl * samtools-0.1.2-6 * improve indel caller by setting maximum window size ------------------------------------------------------------------------ r123 | lh3lh3 | 2009-02-12 10:30:29 +0000 (Thu, 12 Feb 2009) | 2 lines Changed paths: M /trunk/samtools/bam_plcmd.c M /trunk/samtools/bamtk.c * output max mapping quality in indel line ------------------------------------------------------------------------ r122 | lh3lh3 | 2009-02-11 10:59:10 +0000 (Wed, 11 Feb 2009) | 2 lines Changed paths: M /trunk/samtools/misc/maq2sam.c fixed a bug in generating tag AM ------------------------------------------------------------------------ r121 | lh3lh3 | 2009-02-03 10:43:11 +0000 (Tue, 03 Feb 2009) | 2 lines Changed paths: M /trunk/samtools/bam_index.c M /trunk/samtools/bamtk.c fixed a potential memory problem in indexing ------------------------------------------------------------------------ r120 | bhandsaker | 2009-02-02 15:52:52 +0000 (Mon, 02 Feb 2009) | 2 lines Changed paths: M /trunk/samtools/Makefile Pass LIBS to recursive targets to facilitate building at Broad. ------------------------------------------------------------------------ r119 | lh3lh3 | 2009-02-02 10:12:15 +0000 (Mon, 02 Feb 2009) | 4 lines Changed paths: M /trunk/samtools/ChangeLog M /trunk/samtools/bam_plcmd.c M /trunk/samtools/bam_stat.c M /trunk/samtools/bamtk.c * samtools-0.1.2-3 * fixed a bug in generating GLFv2 for indels * improve flagstat report a little bit ------------------------------------------------------------------------ r118 | lh3lh3 | 2009-01-29 12:33:23 +0000 (Thu, 29 Jan 2009) | 3 lines Changed paths: M /trunk/samtools/Makefile A /trunk/samtools/bam_stat.c M /trunk/samtools/bamtk.c * samtools-0.1.2-1 * added flagstat command ------------------------------------------------------------------------ r116 | lh3lh3 | 2009-01-28 13:31:12 +0000 (Wed, 28 Jan 2009) | 2 lines Changed paths: M /trunk/samtools/ChangeLog M /trunk/samtools/NEWS M /trunk/samtools/bamtk.c M /trunk/samtools/samtools.1 Release SAMtools-0.1.2 ------------------------------------------------------------------------ r115 | lh3lh3 | 2009-01-28 12:54:08 +0000 (Wed, 28 Jan 2009) | 2 lines Changed paths: A /trunk/samtools/misc/indel_filter.pl Script for filtering indel results ------------------------------------------------------------------------ r114 | lh3lh3 | 2009-01-25 11:45:37 +0000 (Sun, 25 Jan 2009) | 2 lines Changed paths: A /trunk/samtools/misc/zoom2sam.pl convert ZOOM to SAM ------------------------------------------------------------------------ r113 | lh3lh3 | 2009-01-24 14:25:07 +0000 (Sat, 24 Jan 2009) | 2 lines Changed paths: A /trunk/samtools/misc/novo2sam.pl add a script to convert novo alignment to SAM ------------------------------------------------------------------------ r112 | lh3lh3 | 2009-01-23 20:57:39 +0000 (Fri, 23 Jan 2009) | 2 lines Changed paths: M /trunk/samtools/ChangeLog M /trunk/samtools/ChangeLog.old M /trunk/samtools/samtools.1 update documentation and ChangeLog ------------------------------------------------------------------------ r111 | lh3lh3 | 2009-01-23 19:22:59 +0000 (Fri, 23 Jan 2009) | 3 lines Changed paths: M /trunk/samtools/bam_sort.c M /trunk/samtools/bamtk.c * samtools-0.1.1-19 * fixed a bug in "merge" command line ------------------------------------------------------------------------ r110 | lh3lh3 | 2009-01-22 15:36:48 +0000 (Thu, 22 Jan 2009) | 3 lines Changed paths: M /trunk/samtools/misc/Makefile A /trunk/samtools/misc/bowtie2sam.pl (from /branches/dev/samtools/misc/bowtie2sam.pl:108) M /trunk/samtools/misc/export2sam.pl A /trunk/samtools/misc/soap2sam.pl (from /branches/dev/samtools/misc/soap2sam.pl:108) A /trunk/samtools/misc/wgsim.c (from /branches/dev/samtools/misc/wgsim.c:108) A /trunk/samtools/misc/wgsim_eval.pl (from /branches/dev/samtools/misc/wgsim_eval.pl:108) * merge from branches/dev/ * all future development will happen here ------------------------------------------------------------------------ r109 | lh3lh3 | 2009-01-22 15:14:27 +0000 (Thu, 22 Jan 2009) | 3 lines Changed paths: M /trunk/samtools/COPYING M /trunk/samtools/ChangeLog A /trunk/samtools/INSTALL (from /branches/dev/samtools/INSTALL:108) M /trunk/samtools/Makefile A /trunk/samtools/Makefile.lite (from /branches/dev/samtools/Makefile.lite:108) M /trunk/samtools/bam.c M /trunk/samtools/bam.h M /trunk/samtools/bam_import.c M /trunk/samtools/bam_index.c M /trunk/samtools/bam_lpileup.c M /trunk/samtools/bam_maqcns.c M /trunk/samtools/bam_maqcns.h A /trunk/samtools/bam_mate.c (from /branches/dev/samtools/bam_mate.c:108) M /trunk/samtools/bam_pileup.c M /trunk/samtools/bam_plcmd.c A /trunk/samtools/bam_rmdup.c (from /branches/dev/samtools/bam_rmdup.c:108) M /trunk/samtools/bam_sort.c M /trunk/samtools/bamtk.c M /trunk/samtools/bgzf.h M /trunk/samtools/examples/00README.txt A /trunk/samtools/examples/Makefile (from /branches/dev/samtools/examples/Makefile:108) D /trunk/samtools/examples/ex1.fa.fai M /trunk/samtools/examples/ex1.sam.gz M /trunk/samtools/faidx.c A /trunk/samtools/glf.c (from /branches/dev/samtools/glf.c:108) M /trunk/samtools/glf.h M /trunk/samtools/misc/Makefile M /trunk/samtools/misc/maq2sam.c M /trunk/samtools/razf.c M /trunk/samtools/source.dot * Merge from branches/dev/ * all future development will happen here at trunk/ ------------------------------------------------------------------------ r79 | bhandsaker | 2009-01-07 21:42:15 +0000 (Wed, 07 Jan 2009) | 2 lines Changed paths: M /trunk/samtools/bam_maqcns.c M /trunk/samtools/bam_tview.c Fix problem with compiling without curses. ------------------------------------------------------------------------ r63 | lh3lh3 | 2008-12-22 15:58:02 +0000 (Mon, 22 Dec 2008) | 2 lines Changed paths: A /trunk/samtools (from /branches/dev/samtools:62) Create trunk copy ------------------------------------------------------------------------ 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) ------------------------------------------------------------------------