X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ChangeLog;h=fe2a947cba1ed55ca5ed2fea60799c63f149743e;hb=b0ed19dc2d8fb84998d41d6c3588611185707137;hp=07355572bf52407650bf22bd28a749d83819ef7e;hpb=6d1982a4077cd49500453360d2a497d38cb63522;p=samtools.git

diff --git a/ChangeLog b/ChangeLog
index 0735557..fe2a947 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,839 @@
+------------------------------------------------------------------------
+r296 | lh3lh3 | 2009-05-21 12:53:14 +0100 (Thu, 21 May 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_maqcns.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-24 (r296)
+ * another similar bug in the indel caller
+
+------------------------------------------------------------------------
+r295 | lh3lh3 | 2009-05-21 12:50:28 +0100 (Thu, 21 May 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_maqcns.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-23 (r295)
+ * fixed a critical bug in the indel caller
+
+------------------------------------------------------------------------
+r294 | lh3lh3 | 2009-05-20 13:00:20 +0100 (Wed, 20 May 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_stat.c
+
+added a missing header file
+
+------------------------------------------------------------------------
+r293 | lh3lh3 | 2009-05-19 23:44:25 +0100 (Tue, 19 May 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_tview.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-22 (r293)
+ * open tview in the dot-view mode by default
+
+------------------------------------------------------------------------
+r292 | lh3lh3 | 2009-05-18 21:01:23 +0100 (Mon, 18 May 2009) | 6 lines
+Changed paths:
+   M /trunk/samtools/samtools.1
+
+Added a note to the manual. Currently SAMtools used unaligned words in
+several places. Although this does not cause bus errors to me, it may
+affect portability. Please see the "Bus error" wiki page for more
+information. Also thank James Bonfields for pointing this out.
+
+
+------------------------------------------------------------------------
+r286 | lh3lh3 | 2009-05-14 15:23:13 +0100 (Thu, 14 May 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam.h
+   M /trunk/samtools/bam_aux.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-21 (286)
+ * declare bam_aux_get_core() in bam.h
+
+------------------------------------------------------------------------
+r276 | lh3lh3 | 2009-05-13 10:07:55 +0100 (Wed, 13 May 2009) | 5 lines
+Changed paths:
+   M /trunk/samtools/bam.h
+   M /trunk/samtools/bam_index.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-20 (r276)
+ * remove bam1_t::hash again. We need to modify the Perl API anyway to
+   make it work with the latest SVN.
+ * As is suggested by Tim, scan "{base}.bai" and "{base}.bam.bai" for index
+
+------------------------------------------------------------------------
+r275 | lh3lh3 | 2009-05-12 21:14:10 +0100 (Tue, 12 May 2009) | 4 lines
+Changed paths:
+   M /trunk/samtools/ChangeLog
+   M /trunk/samtools/bam.h
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-19 (r275)
+ * a minor change to the bam1_t struct: added back "void *hash" for the
+   backward compatibility with Bio::DB::Sam
+
+------------------------------------------------------------------------
+r273 | lh3lh3 | 2009-05-12 14:28:39 +0100 (Tue, 12 May 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_rmdupse.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-18 (r273)
+ * rmdupse: do not remove unmapped reads
+
+------------------------------------------------------------------------
+r272 | lh3lh3 | 2009-05-12 14:20:00 +0100 (Tue, 12 May 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_rmdupse.c
+
+change a parameter. It does nothing
+
+------------------------------------------------------------------------
+r271 | lh3lh3 | 2009-05-12 14:17:58 +0100 (Tue, 12 May 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/Makefile.am
+   M /trunk/samtools/Makefile.generic
+   M /trunk/samtools/Makefile.lite
+   A /trunk/samtools/bam_rmdupse.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/configure.ac
+
+ * samtools-0.1.3-17 (r271)
+ * added 'rmdupse' command
+
+------------------------------------------------------------------------
+r267 | lh3lh3 | 2009-05-05 22:31:41 +0100 (Tue, 05 May 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.3-16 (r267)
+ * in sam_view.c, changed g_flag_on based on the suggestion by Angie Hinrichs
+
+------------------------------------------------------------------------
+r266 | lh3lh3 | 2009-05-05 22:23:27 +0100 (Tue, 05 May 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_import.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-15 (r266)
+ * report an error if a non-* reference is present while @SQ is absent
+
+------------------------------------------------------------------------
+r265 | lh3lh3 | 2009-05-05 22:09:00 +0100 (Tue, 05 May 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam.h
+   M /trunk/samtools/bam_import.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/sam.c
+   M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.3-14 (r262)
+ * make samopen() recognize @SQ header lines
+
+------------------------------------------------------------------------
+r261 | lh3lh3 | 2009-05-05 15:10:30 +0100 (Tue, 05 May 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/bgzf.c
+   M /trunk/samtools/sam.c
+   M /trunk/samtools/sam_view.c
+
+ * samtools-0.1.3-13 (r260)
+ * report error for file I/O error
+
+------------------------------------------------------------------------
+r260 | lh3lh3 | 2009-05-05 15:01:16 +0100 (Tue, 05 May 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/Makefile.am
+
+update Makefile.am
+
+------------------------------------------------------------------------
+r259 | lh3lh3 | 2009-05-05 14:52:25 +0100 (Tue, 05 May 2009) | 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
+   M /trunk/samtools/sam.c
+   M /trunk/samtools/sam.h
+
+ * samtools-0.1.3-12 (r259)
+ * use the new I/O interface in pileup
+
+------------------------------------------------------------------------
+r258 | lh3lh3 | 2009-05-05 14:33:22 +0100 (Tue, 05 May 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/Makefile.generic
+   M /trunk/samtools/Makefile.lite
+   M /trunk/samtools/bam.c
+   M /trunk/samtools/bam.h
+   M /trunk/samtools/bam_import.c
+   M /trunk/samtools/bamtk.c
+   A /trunk/samtools/sam.c
+   A /trunk/samtools/sam.h
+   A /trunk/samtools/sam_view.c
+
+ * samtools-0.1.3-11 (r258)
+ * unify the interface to BAM and SAM I/O
+
+------------------------------------------------------------------------
+r257 | lh3lh3 | 2009-05-05 09:53:35 +0100 (Tue, 05 May 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/Makefile.lite
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-10 (r257)
+ * allow hex with "pileup -m"
+
+------------------------------------------------------------------------
+r256 | lh3lh3 | 2009-05-04 19:16:50 +0100 (Mon, 04 May 2009) | 4 lines
+Changed paths:
+   M /trunk/samtools/bam_lpileup.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-9 (r256)
+ * fixed a bug in bam_lpileup.c
+ * I do not know if this also fixes the bug causing assertion failure in the tview
+
+------------------------------------------------------------------------
+r251 | lh3lh3 | 2009-04-28 13:53:23 +0100 (Tue, 28 Apr 2009) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_pileup.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.3-8 (r251)
+ * fixed a bug when there are reads without coordinates
+
+------------------------------------------------------------------------
+r250 | lh3lh3 | 2009-04-28 13:43:33 +0100 (Tue, 28 Apr 2009) | 2 lines
+Changed paths:
+   A /trunk/samtools/AUTHORS
+   A /trunk/samtools/README
+   M /trunk/samtools/cleanup.sh
+
+added missing files
+
+------------------------------------------------------------------------
+r249 | lh3lh3 | 2009-04-28 13:37:16 +0100 (Tue, 28 Apr 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/Makefile.generic
+   M /trunk/samtools/Makefile.lite
+   M /trunk/samtools/configure.ac
+   M /trunk/samtools/misc/Makefile.generic
+
+improve large file support in compilation
+
+------------------------------------------------------------------------
+r248 | lh3lh3 | 2009-04-28 13:33:24 +0100 (Tue, 28 Apr 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/INSTALL
+
+update INSTALL
+
+------------------------------------------------------------------------
+r247 | lh3lh3 | 2009-04-28 13:28:50 +0100 (Tue, 28 Apr 2009) | 2 lines
+Changed paths:
+   M /trunk/samtools/Makefile.am
+   M /trunk/samtools/autogen.sh
+   M /trunk/samtools/cleanup.sh
+   M /trunk/samtools/configure.ac
+   A /trunk/samtools/misc/Makefile.am
+
+fixed various issues about the GNU building scripts
+
+------------------------------------------------------------------------
+r246 | lh3lh3 | 2009-04-28 13:10:23 +0100 (Tue, 28 Apr 2009) | 4 lines
+Changed paths:
+   M /trunk/samtools/ChangeLog
+   D /trunk/samtools/Makefile
+   A /trunk/samtools/Makefile.am
+   A /trunk/samtools/Makefile.generic
+   A /trunk/samtools/autogen.sh
+   M /trunk/samtools/bam.h
+   M /trunk/samtools/bam_aux.c
+   M /trunk/samtools/bam_tview.c
+   M /trunk/samtools/bamtk.c
+   A /trunk/samtools/cleanup.sh
+   A /trunk/samtools/configure.ac
+   D /trunk/samtools/misc/Makefile
+   A /trunk/samtools/misc/Makefile.generic (from /trunk/samtools/misc/Makefile:245)
+
+ * samtools-0.1.3-7 (r246)
+ * incorporated revisions from Nils Homer
+ * enhanced support of displaying color-space reads
+
+------------------------------------------------------------------------
+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: