+r612 | lh3lh3 | 2010-07-11 21:08:56 -0400 (Sun, 11 Jul 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/knetfile.c
+
+fixed a compiling issue for Windows
+
+------------------------------------------------------------------------
+r611 | lh3lh3 | 2010-07-11 20:59:15 -0400 (Sun, 11 Jul 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_sort.c
+
+fixed a bug in sorting when output to stdout (by Peter Chines)
+
+------------------------------------------------------------------------
+r610 | lh3lh3 | 2010-07-09 17:05:10 -0400 (Fri, 09 Jul 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/NEWS
+ M /trunk/samtools/bam_plcmd.c
+
+change the command line option of pileup
+
+------------------------------------------------------------------------
+r609 | lh3lh3 | 2010-07-09 00:39:34 -0400 (Fri, 09 Jul 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_pileup.c
+ A /trunk/samtools/examples/toy.fa
+ A /trunk/samtools/examples/toy.sam
+
+make pileup work with CIGAR with I/D at the beginning or in the end
+
+------------------------------------------------------------------------
+r608 | lh3lh3 | 2010-07-08 22:36:12 -0400 (Thu, 08 Jul 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_maqcns.h
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bam_tview.c
+
+ * make tview more friendly
+ * a temporary remedy for an issue in indel calling
+
+------------------------------------------------------------------------
+r607 | lh3lh3 | 2010-07-08 14:43:52 -0400 (Thu, 08 Jul 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-r607
+ * improved the genotype accuracy for indels
+ * use the SOAPsnp model for SNP calling by default.
+
+------------------------------------------------------------------------
+r606 | lh3lh3 | 2010-07-08 01:05:19 -0400 (Thu, 08 Jul 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/misc/Makefile
+
+removed a debugging example
+
+------------------------------------------------------------------------
+r605 | lh3lh3 | 2010-07-08 01:04:09 -0400 (Thu, 08 Jul 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-.1.7-18 (r605)
+ * fixed an issue when a deletion and mismatch occur at the same time
+ and the base quality is higher than 40 (if -I40).
+
+------------------------------------------------------------------------
+r604 | lh3lh3 | 2010-07-02 19:32:24 -0400 (Fri, 02 Jul 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/misc/Makefile
+
+fixed a minor bug in idxstats
+
+------------------------------------------------------------------------
+r601 | lh3lh3 | 2010-06-16 09:03:59 -0400 (Wed, 16 Jun 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+
+fixed a minor bug in indexing
+
+------------------------------------------------------------------------
+r600 | lh3lh3 | 2010-06-15 10:17:53 -0400 (Tue, 15 Jun 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/bam.c
+
+change printf() to puts in exporting
+
+------------------------------------------------------------------------
+r599 | lh3lh3 | 2010-06-13 21:41:11 -0400 (Sun, 13 Jun 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+
+minor fix. No actual effect.
+
+------------------------------------------------------------------------
+r598 | lh3lh3 | 2010-06-13 21:32:45 -0400 (Sun, 13 Jun 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+
+added Makefile targets to compile shared/dynamic library
+
+------------------------------------------------------------------------
+r596 | lh3lh3 | 2010-06-13 19:48:07 -0400 (Sun, 13 Jun 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-17 (r596)
+ * also keep the number of coor-less reads in the index file
+
+------------------------------------------------------------------------
+r595 | lh3lh3 | 2010-06-13 18:54:26 -0400 (Sun, 13 Jun 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-16 (r595)
+ * write additional information to bam index
+
+------------------------------------------------------------------------
+r594 | lh3lh3 | 2010-06-13 17:29:52 -0400 (Sun, 13 Jun 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+
+fixed a bug for unmapped sequences in indexing
+
+------------------------------------------------------------------------
+r593 | lh3lh3 | 2010-06-12 18:11:32 -0400 (Sat, 12 Jun 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/samtools.1
+
+rename iterf as iter
+
+------------------------------------------------------------------------
+r592 | lh3lh3 | 2010-06-12 18:02:38 -0400 (Sat, 12 Jun 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/bam_aux.c
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-15 (r592)
+ * fixed a few minor memory leaks in the new pileup code
+ * improved the functionality of mpileup
+
+------------------------------------------------------------------------
+r591 | lh3lh3 | 2010-06-12 14:09:22 -0400 (Sat, 12 Jun 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-14 (r591)
+ * elementary multi-way pileup. More testing and more functionality to be done.
+
+------------------------------------------------------------------------
+r590 | lh3lh3 | 2010-06-12 01:00:24 -0400 (Sat, 12 Jun 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-13 (r590)
+ * added mpileup APIs. No compiling errors, but not tested at all. It is late.
+
+------------------------------------------------------------------------
+r589 | lh3lh3 | 2010-06-11 22:37:09 -0400 (Fri, 11 Jun 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_pileup.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-12 (r589)
+ * added iterator-like APIs for pileup
+
+------------------------------------------------------------------------
+r588 | lh3lh3 | 2010-06-11 17:41:13 -0400 (Fri, 11 Jun 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-11 (r588)
+ * ported a few improvements from tabix back to samtools
+
+------------------------------------------------------------------------
+r587 | lh3lh3 | 2010-06-11 17:33:16 -0400 (Fri, 11 Jun 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-10 (r587)
+ * added iterator interface for bam_fetch (ported back from tabix)
+
+------------------------------------------------------------------------
+r586 | lh3lh3 | 2010-06-11 13:23:53 -0400 (Fri, 11 Jun 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ A /trunk/samtools/bam_reheader.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bgzf.c
+
+ * samtools-0.1.7-9 (r586)
+ * added "reheader" to replace the BAM header
+
+------------------------------------------------------------------------
+r585 | lh3lh3 | 2010-06-11 12:22:06 -0400 (Fri, 11 Jun 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/kstring.h
+
+ * samtools-0.1.7-8 (r585)
+ * speed up "view"
+
+------------------------------------------------------------------------
+r584 | lh3lh3 | 2010-06-11 12:00:41 -0400 (Fri, 11 Jun 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/bgzf.c
+ M /trunk/samtools/bgzf.h
+ M /trunk/samtools/kstring.h
+ M /trunk/samtools/misc/wgsim_eval.pl
+
+ * samtools-0.1.7-7 (r584)
+ * ported tabix BGZF to samtools
+ * flush BGZF after writing the BAM header and between alignment boundaries
+
+------------------------------------------------------------------------
+r583 | petulda | 2010-06-11 11:58:20 -0400 (Fri, 11 Jun 2010) | 1 line
+Changed paths:
+ A /trunk/samtools/misc/varfilter.py
+
+Initial release on behalf of Aylwyn Scally
+------------------------------------------------------------------------
+r561 | petulda | 2010-05-07 08:41:56 -0400 (Fri, 07 May 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/samtools.1
+
+Added a note about the indels coordinates
+------------------------------------------------------------------------
+r551 | petulda | 2010-04-23 09:42:13 -0400 (Fri, 23 Apr 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/misc/sam2vcf.pl
+
+Added the possibility to print or not to print the reference allele
+------------------------------------------------------------------------
+r546 | petulda | 2010-04-15 04:33:55 -0400 (Thu, 15 Apr 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/sam_header.c
+
+More descriptive message for space separated tags
+------------------------------------------------------------------------
+r545 | petulda | 2010-04-14 11:44:50 -0400 (Wed, 14 Apr 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/misc/sam2vcf.pl
+
+Speedup with -i, no need to query the reference all the time
+------------------------------------------------------------------------
+r541 | petulda | 2010-03-15 10:03:51 -0400 (Mon, 15 Mar 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/sam_header.c
+
+Fixed the order of sequences in the header
+------------------------------------------------------------------------
+r540 | petulda | 2010-03-04 06:28:35 -0500 (Thu, 04 Mar 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/misc/sam2vcf.pl
+
+Added possibility to select indels only and fixed a bug in reporting homozygous indels.
+------------------------------------------------------------------------
+r539 | jmarshall | 2010-02-27 06:48:17 -0500 (Sat, 27 Feb 2010) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+
+Improve the invalid 'BAM\1' magic number error message, and also print it
+when no bytes can be read from the alleged BAM file, e.g., in the common
+user error case when a SAM file has accidentally been supplied.
+
+------------------------------------------------------------------------
+r538 | petulda | 2010-02-26 10:51:40 -0500 (Fri, 26 Feb 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/AUTHORS
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/sam_header.c
+
+Improved efficiency of header parsing
+------------------------------------------------------------------------
+r537 | lh3lh3 | 2010-02-23 21:08:48 -0500 (Tue, 23 Feb 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/misc/export2sam.pl
+
+Updated export2sam.pl by Chris Saunders from Illumina.
+
+
+------------------------------------------------------------------------
+r536 | petulda | 2010-02-17 08:32:53 -0500 (Wed, 17 Feb 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/misc/samtools.pl
+
+Fixed filtering of SNPs near indels. Added min indel and SNP quality filter.
+------------------------------------------------------------------------
+r535 | petulda | 2010-02-12 04:52:37 -0500 (Fri, 12 Feb 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/misc/sam2vcf.pl
+
+Print an error for pileups in simple format
+------------------------------------------------------------------------
+r534 | lh3lh3 | 2010-02-11 14:01:41 -0500 (Thu, 11 Feb 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+
+added a hidden option in pileup to output the base position (for Erin)
+
+------------------------------------------------------------------------
+r533 | petulda | 2010-02-09 10:12:14 -0500 (Tue, 09 Feb 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/misc/sam2vcf.pl
+
+Added possibility to specify a custom column title for the data column
+------------------------------------------------------------------------
+r532 | petulda | 2010-02-09 09:46:09 -0500 (Tue, 09 Feb 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+
+Added the -d option to limit maximum depth for indels.
+------------------------------------------------------------------------
+r531 | petulda | 2010-02-03 07:57:27 -0500 (Wed, 03 Feb 2010) | 1 line
+Changed paths:
+ M /trunk/samtools/misc/sam2vcf.pl
+
+Added VCF header
+------------------------------------------------------------------------
+r530 | lh3lh3 | 2010-02-01 09:13:19 -0500 (Mon, 01 Feb 2010) | 3 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/misc/samtools.pl
+ M /trunk/samtools/misc/wgsim.c
+
+ * samtools-0.1.7-6
+ * fixed a bug in faidx
+
+------------------------------------------------------------------------
+r529 | jmarshall | 2010-01-11 18:51:49 -0500 (Mon, 11 Jan 2010) | 2 lines
+Changed paths:
+ M /trunk/samtools/faidx.c
+
+Put the right filename in the error message.
+
+------------------------------------------------------------------------
+r528 | lh3lh3 | 2009-12-14 11:26:47 -0500 (Mon, 14 Dec 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-5 (r528)
+ * further add new consensus generation strategy
+
+------------------------------------------------------------------------
+r527 | petulda | 2009-12-11 12:31:05 -0500 (Fri, 11 Dec 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/knetfile.c
+
+Fixed a bug in knet_seek
+------------------------------------------------------------------------
+r526 | petulda | 2009-12-11 07:51:18 -0500 (Fri, 11 Dec 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/misc/sam2vcf.pl
+
+Small fix in VCF format: dot for the empty INFO field
+------------------------------------------------------------------------
+r525 | petulda | 2009-12-11 04:36:18 -0500 (Fri, 11 Dec 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/sam_header.c
+
+Allow tabs in the CO header field
+------------------------------------------------------------------------
+r524 | jmarshall | 2009-12-10 10:03:58 -0500 (Thu, 10 Dec 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/Makefile.mingw
+
+Depend on libbam.a rather than the phony target, so that samtools is not
+unnecessarily rebuilt every time. Also clean bgzip.
+
+------------------------------------------------------------------------
+r523 | jmarshall | 2009-12-10 09:45:32 -0500 (Thu, 10 Dec 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/Makefile.mingw
+
+Fix a bug in compiling bgzip: this also needs knetfile.o when _USE_KNETFILE
+is defined. Also introduce $(KNETFILE_O) which can be set to empty to
+facilitate non-knet builds.
+
+------------------------------------------------------------------------
+r522 | lh3lh3 | 2009-12-01 13:02:36 -0500 (Tue, 01 Dec 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.7-4 (r522)
+ * fixed a bug in "view -r"
+ * added a new option "view -R" to read required read groups from a file
+
+------------------------------------------------------------------------
+r521 | lh3lh3 | 2009-12-01 10:00:12 -0500 (Tue, 01 Dec 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.7-3 (r521)
+ * calmd: optionally mask matching bases as N
+
+------------------------------------------------------------------------
+r520 | lh3lh3 | 2009-12-01 09:37:17 -0500 (Tue, 01 Dec 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/misc/samtools.pl
+
+ * samtools-0.1.7-2 (r520)
+ * fixed a few issues with compilation in Windows (on behalf of John)
+ * choose a random base as the consensus (for population genetics studies)
+
+------------------------------------------------------------------------
+r519 | jmarshall | 2009-11-30 10:53:02 -0500 (Mon, 30 Nov 2009) | 6 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+
+Put libraries at the end, so they can resolve references from libbam.a
+as well, even with old-fashioned linkers.
+
+Also use libbam.a explicitly rather than "-L. -lbam" to ensure that we get
+the freshly built library, not some other libbam.a lying around the system.
+
+------------------------------------------------------------------------
+r518 | jmarshall | 2009-11-30 08:44:56 -0500 (Mon, 30 Nov 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/misc/Makefile
+
+Also clean *.exe (for Cygwin users using this makefile).
+
+------------------------------------------------------------------------
+r517 | jmarshall | 2009-11-30 07:09:04 -0500 (Mon, 30 Nov 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+
+Index files should be opened in binary mode, not text mode.
+
+------------------------------------------------------------------------
+r516 | lh3lh3 | 2009-11-27 15:18:59 -0500 (Fri, 27 Nov 2009) | 2 lines
+Changed paths:
+ A /trunk/samtools/examples/bam2bed.c
+
+another example program
+
+------------------------------------------------------------------------
+r515 | lh3lh3 | 2009-11-27 10:44:56 -0500 (Fri, 27 Nov 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/misc/wgsim_eval.pl
+ M /trunk/samtools/sam.c
+
+ * samtools-0.1.7-1 (r515)
+ * report an error when .fai contains duplicated names, instead of segfault
+
+------------------------------------------------------------------------
+r514 | jmarshall | 2009-11-24 09:45:35 -0500 (Tue, 24 Nov 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+
+Format 'c'-encoded auxiliary fields correctly, as *signed* integers.
+
+------------------------------------------------------------------------
+r513 | lh3lh3 | 2009-11-16 10:13:07 -0500 (Mon, 16 Nov 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile.mingw
+
+Update Makefile.mingw for the same reason
+
+------------------------------------------------------------------------
+r512 | lh3lh3 | 2009-11-16 10:00:08 -0500 (Mon, 16 Nov 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+
+Fixed a bug in compiling razip
+
+------------------------------------------------------------------------
+r510 | lh3lh3 | 2009-11-10 10:55:41 -0500 (Tue, 10 Nov 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-0.1.7 (r510)
+
+------------------------------------------------------------------------
+r509 | lh3lh3 | 2009-11-06 09:17:09 -0500 (Fri, 06 Nov 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-22 (r509)
+ * forget to fix a similar problem in glfgen
+
+------------------------------------------------------------------------
+r508 | lh3lh3 | 2009-11-06 09:06:40 -0500 (Fri, 06 Nov 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.6-21 (r508)
+ * fixed a potential bug in the indel caller towards the end of a chromosome
+
+------------------------------------------------------------------------
+r494 | lh3lh3 | 2009-10-26 11:38:00 -0400 (Mon, 26 Oct 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.6-19 (r494)
+ * allow to convert Illumina quality (64 based) to the BAM quality
+
+------------------------------------------------------------------------
+r493 | lh3lh3 | 2009-10-26 10:24:39 -0400 (Mon, 26 Oct 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/sam.c
+ M /trunk/samtools/sam_header.c
+
+ * samtools-0.1.6-18 (r493)
+ * fixed the bugs due to improperly incorporating Petr's header parser
+ * a little code clean up in sam_header.c
+
+------------------------------------------------------------------------
+r492 | petulda | 2009-10-24 09:43:25 -0400 (Sat, 24 Oct 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/sam_header.c
+
+Added sam_header_line_free call for sam_header_parse2
+------------------------------------------------------------------------
+r491 | lh3lh3 | 2009-10-24 00:50:16 -0400 (Sat, 24 Oct 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/sam_view.c
+
+ * BUGGY VERSION
+ * fixed a minor bug
+
+------------------------------------------------------------------------
+r490 | lh3lh3 | 2009-10-24 00:45:12 -0400 (Sat, 24 Oct 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/sam.c
+
+ * BUGGY VERSION
+ * improved the interface a bit
+ * bug unfixed
+
+------------------------------------------------------------------------
+r489 | lh3lh3 | 2009-10-24 00:41:50 -0400 (Sat, 24 Oct 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/sam_header.c
+ M /trunk/samtools/sam_header.h
+
+ * BUGGY VERSION. Please NOT use it.
+ * Fixed a minor bug, but the major bug is still there.
+
+------------------------------------------------------------------------
+r488 | lh3lh3 | 2009-10-24 00:17:10 -0400 (Sat, 24 Oct 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_aux.c
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bam_rmdup.c
+ M /trunk/samtools/bam_rmdupse.c
+ M /trunk/samtools/kaln.c
+ M /trunk/samtools/sam.c
+ M /trunk/samtools/sam_header.c
+ M /trunk/samtools/sam_header.h
+ M /trunk/samtools/sam_view.c
+
+ * This revision is SERIOUSLY BUGGY. Please NOT use it.
+ * Start to incorporate header parsing from Petr Danecek
+
+------------------------------------------------------------------------
+r487 | petulda | 2009-10-23 11:44:32 -0400 (Fri, 23 Oct 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/sam_header.c
+ M /trunk/samtools/sam_header.h
+
+Now possible to merge multiple HeaderDict dictionaries
+------------------------------------------------------------------------
+r486 | petulda | 2009-10-22 11:46:58 -0400 (Thu, 22 Oct 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/sam_header.c
+
+
+------------------------------------------------------------------------
+r485 | petulda | 2009-10-22 11:41:56 -0400 (Thu, 22 Oct 2009) | 1 line
+Changed paths:
+ A /trunk/samtools/sam_header.c
+ A /trunk/samtools/sam_header.h
+
+
+------------------------------------------------------------------------
+r484 | lh3lh3 | 2009-10-19 14:31:32 -0400 (Mon, 19 Oct 2009) | 5 lines
+Changed paths:
+ M /trunk/samtools/bam_import.c
+ M /trunk/samtools/bam_rmdupse.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/examples/Makefile
+
+ * samtools-0.1.6-17 (r484)
+ * fixed a memory leak in rmdupse
+ * fixed a bug in parsing @RG header lines
+ * test rmdup in examples/
+
+------------------------------------------------------------------------
+r483 | lh3lh3 | 2009-10-19 13:22:48 -0400 (Mon, 19 Oct 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam_rmdup.c
+ M /trunk/samtools/bam_rmdupse.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-16 (r483)
+ * unify the interface of rmdup and rmdupse
+ * a new bug found in rg2lib(). Have not been fixed yet.
+
+------------------------------------------------------------------------
+r482 | lh3lh3 | 2009-10-19 13:03:34 -0400 (Mon, 19 Oct 2009) | 4 lines
+Changed paths:
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_rmdup.c
+ M /trunk/samtools/bam_rmdupse.c
+ M /trunk/samtools/bamtk.c
+ A /trunk/samtools/klist.h
+
+ * samtools-0.1.6-15 (r482)
+ * rewrite rmdupse
+ * rmdupse is now library aware
+
+------------------------------------------------------------------------
+r481 | lh3lh3 | 2009-10-18 00:07:21 -0400 (Sun, 18 Oct 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_rmdup.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-14 (r480)
+ * rmdup is now RG aware
+
+------------------------------------------------------------------------
+r480 | lh3lh3 | 2009-10-17 22:05:20 -0400 (Sat, 17 Oct 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/misc/samtools.pl
+
+added a small unitity to parse SRA XML files
+
+------------------------------------------------------------------------
+r479 | lh3lh3 | 2009-10-17 20:57:26 -0400 (Sat, 17 Oct 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bam_maqcns.h
+ M /trunk/samtools/bam_plcmd.c
+ M /trunk/samtools/bam_sort.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-13 (r479)
+ * merge: optionally use file names as RG tags
+
+------------------------------------------------------------------------
+r478 | lh3lh3 | 2009-10-14 14:18:12 -0400 (Wed, 14 Oct 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/kaln.c
+
+ * samtools-0.1.6-12 (r478)
+ * fixed a bug in the indel caller
+
+------------------------------------------------------------------------
+r477 | lh3lh3 | 2009-10-10 06:12:26 -0400 (Sat, 10 Oct 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-11 (r477)
+ * fixed a bug due to recent change in bam_index.c (thank Nicole Washington for the patch)
+
+------------------------------------------------------------------------
+r476 | petulda | 2009-10-09 11:45:36 -0400 (Fri, 09 Oct 2009) | 1 line
+Changed paths:
+ A /trunk/samtools/misc/sam2vcf.pl
+
+Added the sam2vcf.pl script.
+------------------------------------------------------------------------
+r475 | lh3lh3 | 2009-10-08 10:19:16 -0400 (Thu, 08 Oct 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/Makefile
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/bam.h
+ M /trunk/samtools/bam_maqcns.c
+ M /trunk/samtools/bamtk.c
+ A /trunk/samtools/kaln.c
+ A /trunk/samtools/kaln.h
+
+Unfinished modification. Please do not use this revision...
+
+------------------------------------------------------------------------
+r474 | petulda | 2009-10-08 06:39:54 -0400 (Thu, 08 Oct 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/knetfile.c
+
+Removed the offending knet_seek message.
+------------------------------------------------------------------------
+r473 | petulda | 2009-10-06 09:26:35 -0400 (Tue, 06 Oct 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/knetfile.c
+ M /trunk/samtools/razf.c
+
+Bug fix - faidx on RAZF compressed files now working.
+------------------------------------------------------------------------
+r472 | lh3lh3 | 2009-10-02 08:42:57 -0400 (Fri, 02 Oct 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/samtools.1
+
+Clarify the meaning of a region like "chr2:1,000,000".
+
+------------------------------------------------------------------------
+r471 | lh3lh3 | 2009-10-02 05:42:19 -0400 (Fri, 02 Oct 2009) | 2 lines
+Changed paths:
+ M /trunk/samtools/misc/novo2sam.pl
+
+Fixed minor bugs in novo2sam.pl (on behalf of Ken Chen and Colin Hercus)
+
+------------------------------------------------------------------------
+r470 | lh3lh3 | 2009-09-29 15:01:27 -0400 (Tue, 29 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/Makefile.mingw
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/knetfile.c
+ M /trunk/samtools/knetfile.h
+
+ * samtools-0.1.6-9 (r470)
+ * make knetfile.c compatible with MinGW (thank Martin Morgan for the patch)
+
+------------------------------------------------------------------------
+r469 | lh3lh3 | 2009-09-29 08:07:44 -0400 (Tue, 29 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_index.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-9 (r469)
+ * refactor bam_fetch() for Python binding. On behalf of Leo Goodstadt.
+
+------------------------------------------------------------------------
+r468 | lh3lh3 | 2009-09-28 05:18:29 -0400 (Mon, 28 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam_sort.c
+ M /trunk/samtools/bamtk.c
+ M /trunk/samtools/misc/samtools.pl
+
+ * samtools-0.1.6-7 (r468)
+ * make merge stable
+
+------------------------------------------------------------------------
+r467 | petulda | 2009-09-28 04:51:29 -0400 (Mon, 28 Sep 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/bgzf.c
+ M /trunk/samtools/bgzip.c
+ M /trunk/samtools/razf.c
+ M /trunk/samtools/razip.c
+
+Changed the mode for newly created files to 0666. This allows less strict permissions with umask properly set (e.g. 0002 vs. 0022).
+------------------------------------------------------------------------
+r466 | lh3lh3 | 2009-09-24 06:29:19 -0400 (Thu, 24 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/ChangeLog
+ M /trunk/samtools/bam_md.c
+ M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.6-6 (r466)
+ * do not crash calmd when some sequences are absent from the reference.
+
+------------------------------------------------------------------------
+r464 | jmarshall | 2009-09-23 06:14:32 -0400 (Wed, 23 Sep 2009) | 3 lines
+Changed paths:
+ M /trunk/samtools/bam.c
+ M /trunk/samtools/knetfile.c
+
+Suppress bgzf_check_EOF() messages when reading from a pipe, as there is
+no way to seek on a pipe and the messages always appear.
+
+------------------------------------------------------------------------
+r463 | petulda | 2009-09-16 07:05:41 -0400 (Wed, 16 Sep 2009) | 1 line
+Changed paths:
+ M /trunk/samtools/knetfile.c
+ M /trunk/samtools/razf.c
+
+A bug fix, "samtools view" is now working again.
+------------------------------------------------------------------------
+r462 | lh3lh3 | 2009-09-16 04:51:07 -0400 (Wed, 16 Sep 2009) | 3 lines