X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=ChangeLog;h=6324ec8b64c79278c794e067eda3eb751cc8f19a;hb=5f33ece1c399de9f1522383ea3b94284989c0e3f;hp=a1beffd4dafdf3940ae567863815464117ba6dee;hpb=e252a356ce3760b7cddf1ed2a5e4374e63864d0d;p=samtools.git

diff --git a/ChangeLog b/ChangeLog
index a1beffd..6324ec8 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,600 @@
+------------------------------------------------------------------------
+r896 | lh3lh3 | 2011-01-06 10:52:15 -0500 (Thu, 06 Jan 2011) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/bcftools/bcf.h
+   M /trunk/samtools/bcftools/bcfutils.c
+   M /trunk/samtools/bcftools/call1.c
+
+ * samtools-0.1.12-10 (r896)
+ * allow to exclude read groups in mpileup
+
+------------------------------------------------------------------------
+r895 | lh3lh3 | 2011-01-04 11:31:29 -0500 (Tue, 04 Jan 2011) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/bcf.tex
+
+sorry. It is SP not ST
+
+------------------------------------------------------------------------
+r894 | lh3lh3 | 2011-01-04 11:29:06 -0500 (Tue, 04 Jan 2011) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/bcf.tex
+
+added ST
+
+------------------------------------------------------------------------
+r893 | petulda | 2011-01-04 06:55:56 -0500 (Tue, 04 Jan 2011) | 1 line
+Changed paths:
+   M /trunk/samtools/bcftools/call1.c
+
+Fixed a typo in read_samples
+------------------------------------------------------------------------
+r892 | jmarshall | 2010-12-28 08:06:49 -0500 (Tue, 28 Dec 2010) | 9 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+   M /trunk/samtools/bcftools/Makefile
+   M /trunk/samtools/examples/Makefile
+
+System libraries go *after* user libraries in link commands, because
+the user libraries may themselves have dependencies that are satisfied
+by the system libraries.  It's not rocket science!
+
+This makes a difference with some linkers; or with -static or --as-needed.
+
+The examples/Makefile fix is from Charles Plessy.
+See also http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=606004
+
+------------------------------------------------------------------------
+r891 | lh3lh3 | 2010-12-21 12:16:33 -0500 (Tue, 21 Dec 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/bcftools/bcf.h
+   M /trunk/samtools/bcftools/bcfutils.c
+   M /trunk/samtools/bcftools/call1.c
+
+ * samtools-0.1.12-9 (r891)
+ * allow to call SNPs from a subset of samples
+
+------------------------------------------------------------------------
+r889 | lh3lh3 | 2010-12-15 11:28:16 -0500 (Wed, 15 Dec 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.12-12 (r889)
+ * set mapQ as 20 if it equals 255
+
+------------------------------------------------------------------------
+r888 | lh3lh3 | 2010-12-14 22:41:09 -0500 (Tue, 14 Dec 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+
+When -B is applied to mpileup, still use paired reads only unless -A is flagged.
+
+------------------------------------------------------------------------
+r887 | lh3lh3 | 2010-12-14 22:37:05 -0500 (Tue, 14 Dec 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_md.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.12-6 (r887)
+ * added a hidden option -E to mpileup/calmd. -E triggers an alternative way to apply BAQ.
+
+------------------------------------------------------------------------
+r886 | lh3lh3 | 2010-12-14 12:51:03 -0500 (Tue, 14 Dec 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bamtk.c
+
+(Arguably) improved the indel caller a tiny bit for lowCov data.
+
+------------------------------------------------------------------------
+r885 | petulda | 2010-12-14 04:55:46 -0500 (Tue, 14 Dec 2010) | 1 line
+Changed paths:
+   M /trunk/samtools/bcftools/call1.c
+
+Fixed the VCF header to pass validation
+------------------------------------------------------------------------
+r884 | lh3lh3 | 2010-12-12 23:02:19 -0500 (Sun, 12 Dec 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/bcftools/vcfutils.pl
+
+ * samtools-0.1.12-4 (r884)
+ * fixed a long-existing flaw in the INDEL calling model
+
+------------------------------------------------------------------------
+r883 | lh3lh3 | 2010-12-11 20:05:42 -0500 (Sat, 11 Dec 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/bcfutils.c
+   M /trunk/samtools/bcftools/call1.c
+   M /trunk/samtools/bcftools/vcfutils.pl
+
+compute max SP and max GQ from sample genotypes
+
+------------------------------------------------------------------------
+r880 | lh3lh3 | 2010-12-10 10:50:54 -0500 (Fri, 10 Dec 2010) | 2 lines
+Changed paths:
+   D /trunk/samtools/bcftools/bcf-fix.pl
+
+drop bcf-fix.pl as it is redundant by the latest changes
+
+------------------------------------------------------------------------
+r879 | lh3lh3 | 2010-12-10 10:50:29 -0500 (Fri, 10 Dec 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bcftools/call1.c
+   M /trunk/samtools/bcftools/vcf.c
+
+ * fixed a minor issue in printing VCFs
+ * write bcftools specific INFO and FORMAT in the header
+
+------------------------------------------------------------------------
+r878 | lh3lh3 | 2010-12-10 10:09:14 -0500 (Fri, 10 Dec 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/bcftools/bcfutils.c
+   M /trunk/samtools/bcftools/call1.c
+
+Make sure that the GT genotype field is the first
+
+------------------------------------------------------------------------
+r877 | lh3lh3 | 2010-12-08 17:27:05 -0500 (Wed, 08 Dec 2010) | 7 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf.h
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.12-2 (r877)
+
+ * allow to fine control the selection of indel candidates. The current
+   setting is okay for lowCov and highCov with ~100 samples, but it
+   skips too many indels for highCov with >250 samples.
+
+
+------------------------------------------------------------------------
+r874 | lh3lh3 | 2010-12-07 22:40:35 -0500 (Tue, 07 Dec 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_plcmd.c
+
+a spelling error..
+
+------------------------------------------------------------------------
+r873 | lh3lh3 | 2010-12-07 22:39:57 -0500 (Tue, 07 Dec 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.12-1 (r873)
+ * added a switch to allow anomalous read pairs in calling
+
+------------------------------------------------------------------------
+r872 | lh3lh3 | 2010-12-07 14:43:54 -0500 (Tue, 07 Dec 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/vcfutils.pl
+
+fixed a bug in vcf2fq
+
+------------------------------------------------------------------------
+r869 | lh3lh3 | 2010-12-05 01:18:06 -0500 (Sun, 05 Dec 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bamtk.c
+
+added a warning for the Windows version
+
+------------------------------------------------------------------------
+r868 | lh3lh3 | 2010-12-05 01:05:51 -0500 (Sun, 05 Dec 2010) | 4 lines
+Changed paths:
+   M /trunk/samtools/bcftools/call1.c
+
+In ksprintf(), change "%lf" and "%lg" to "%f" and "%g", respectively.
+According to the manual page, this change is valid. However, MinGW seems
+to interpret "%lf" as "%Lf".
+
+------------------------------------------------------------------------
+r867 | lh3lh3 | 2010-12-05 00:35:43 -0500 (Sun, 05 Dec 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/Makefile.mingw
+   M /trunk/samtools/bam_aux.c
+
+bring back the windows support
+
+------------------------------------------------------------------------
+r866 | lh3lh3 | 2010-12-04 23:33:51 -0500 (Sat, 04 Dec 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_reheader.c
+   M /trunk/samtools/bcftools/vcfutils.pl
+
+Fixed a compiling error when knetfile is not used.
+
+------------------------------------------------------------------------
+r865 | lh3lh3 | 2010-12-04 00:13:22 -0500 (Sat, 04 Dec 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/vcfutils.pl
+
+vcf->fastq
+
+------------------------------------------------------------------------
+r864 | lh3lh3 | 2010-12-03 17:12:30 -0500 (Fri, 03 Dec 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bcftools/call1.c
+   M /trunk/samtools/bcftools/prob1.c
+   M /trunk/samtools/bcftools/prob1.h
+
+ * remove "-f". Instead always compute consensus quality
+ * increase the upper limit of quality
+
+------------------------------------------------------------------------
+r863 | lh3lh3 | 2010-12-03 15:28:15 -0500 (Fri, 03 Dec 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/bcf.c
+
+more informative error message
+
+------------------------------------------------------------------------
+r862 | lh3lh3 | 2010-12-02 16:16:08 -0500 (Thu, 02 Dec 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/NEWS
+   M /trunk/samtools/bamtk.c
+
+Release samtools-0.1.12a
+
+------------------------------------------------------------------------
+r861 | lh3lh3 | 2010-12-02 15:55:06 -0500 (Thu, 02 Dec 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/call1.c
+
+a possible fix to DP4=0,0,0,0; have not tested, but should have no side-effect
+
+------------------------------------------------------------------------
+r859 | lh3lh3 | 2010-12-02 11:39:57 -0500 (Thu, 02 Dec 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/NEWS
+   M /trunk/samtools/bam_index.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/samtools.1
+
+Release samtools-0.1.12
+
+------------------------------------------------------------------------
+r858 | lh3lh3 | 2010-12-02 11:24:41 -0500 (Thu, 02 Dec 2010) | 4 lines
+Changed paths:
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/bcftools/bcf.c
+
+ * samtools-0.1.11-1 (r858)
+ * fixed a bug in mpileup which causes segfaults
+ * bcftools: do not segfault when BCF contains errors
+
+------------------------------------------------------------------------
+r857 | lh3lh3 | 2010-11-30 23:52:50 -0500 (Tue, 30 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_index.c
+
+fixed a memory leak in bam_fetch()
+
+------------------------------------------------------------------------
+r856 | lh3lh3 | 2010-11-26 00:07:31 -0500 (Fri, 26 Nov 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bcftools/vcfutils.pl
+
+ * fixed a memory violation
+ * added splitchr to vcfutils.pl
+
+------------------------------------------------------------------------
+r854 | lh3lh3 | 2010-11-23 09:05:08 -0500 (Tue, 23 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/ld.c
+
+fixed a typo/bug in r^2 computation
+
+------------------------------------------------------------------------
+r852 | lh3lh3 | 2010-11-21 22:20:20 -0500 (Sun, 21 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bamtk.c
+
+forget to change the version information
+
+------------------------------------------------------------------------
+r851 | lh3lh3 | 2010-11-21 22:16:52 -0500 (Sun, 21 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/ChangeLog
+   M /trunk/samtools/NEWS
+   M /trunk/samtools/bcftools/bcftools.1
+   M /trunk/samtools/samtools.1
+
+Release samtools-0.1.11
+
+------------------------------------------------------------------------
+r844 | lh3lh3 | 2010-11-19 23:16:08 -0500 (Fri, 19 Nov 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/bcftools/call1.c
+   M /trunk/samtools/bcftools/prob1.c
+   M /trunk/samtools/bcftools/prob1.h
+
+ * samtools-0.1.10-9 (r844)
+ * added the "folded" or reference-free mode for variant calling
+
+------------------------------------------------------------------------
+r843 | lh3lh3 | 2010-11-19 22:26:36 -0500 (Fri, 19 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/NEWS
+   M /trunk/samtools/bam_sort.c
+
+In merging, if -R is specified, do not abort if the sequence dictionary is different.
+
+------------------------------------------------------------------------
+r842 | jmarshall | 2010-11-19 21:24:28 -0500 (Fri, 19 Nov 2010) | 5 lines
+Changed paths:
+   M /trunk/samtools/bam_sort.c
+
+When merging BAM headers, compare the list of target reference sequences
+strictly (and fail/abort if there is a mismatch), but allow one list to be a
+prefix of the other.  (i.e., check that the lists are identical up until the
+shorter runs out, and add the excess targets from the longer to the output.)
+
+------------------------------------------------------------------------
+r841 | lh3lh3 | 2010-11-19 14:49:27 -0500 (Fri, 19 Nov 2010) | 4 lines
+Changed paths:
+   M /trunk/samtools/bam_index.c
+   M /trunk/samtools/bam_pileup.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.10 (r841)
+ * fixed a bug in pileup when the first CIGAR operation is D
+ * fixed a bug in view with range query
+
+------------------------------------------------------------------------
+r840 | lh3lh3 | 2010-11-19 13:45:51 -0500 (Fri, 19 Nov 2010) | 10 lines
+Changed paths:
+   M /trunk/samtools/ChangeLog
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf.h
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.10-4 (r840)
+
+ * drop the MNP caller. It is slow while does not diliver too much
+   benefit. Possibly I will work on it in future given more time.
+
+ * there is a segfault in pileup 
+
+ * someone has reported segfault from view/index/sort
+
+
+------------------------------------------------------------------------
+r839 | lh3lh3 | 2010-11-18 17:30:11 -0500 (Thu, 18 Nov 2010) | 9 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.h
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.10-6 (r839)
+
+ * call MNPs without realignment because it seems to me that it is not
+   worthwhile to significantly slow down SNP calling.
+
+ * the result looks quite different from the previous version. I have
+   work to do...
+
+
+------------------------------------------------------------------------
+r838 | lh3lh3 | 2010-11-18 11:26:09 -0500 (Thu, 18 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/knetfile.c
+
+Apply a patch by Rob Davis, which improves fault detection.
+
+------------------------------------------------------------------------
+r836 | lh3lh3 | 2010-11-18 11:09:23 -0500 (Thu, 18 Nov 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-r836
+ * initiate MNP realignment when the MNP has at least 0.2% frequency (otherwise too slow)
+
+------------------------------------------------------------------------
+r835 | lh3lh3 | 2010-11-18 00:25:13 -0500 (Thu, 18 Nov 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bcftools/vcfutils.pl
+
+ * modify the filtering rule: also filter SNPs around filtered indels
+ * added MNP filter
+
+------------------------------------------------------------------------
+r834 | lh3lh3 | 2010-11-17 23:13:52 -0500 (Wed, 17 Nov 2010) | 4 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.10-4 (r834)
+ * fixed a silly bug in printing MNP
+ * restrict to at most 1 alternative allele
+
+------------------------------------------------------------------------
+r833 | lh3lh3 | 2010-11-17 21:58:58 -0500 (Wed, 17 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bamtk.c
+
+fixed a bug in printing MNPs
+
+------------------------------------------------------------------------
+r832 | lh3lh3 | 2010-11-17 21:47:20 -0500 (Wed, 17 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bamtk.c
+
+minor change to how seqQ is applied
+
+------------------------------------------------------------------------
+r831 | lh3lh3 | 2010-11-17 21:41:12 -0500 (Wed, 17 Nov 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf.h
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.10 (r831)
+ * initial MNP caller
+
+------------------------------------------------------------------------
+r829 | lh3lh3 | 2010-11-16 23:14:15 -0500 (Tue, 16 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/ChangeLog
+   M /trunk/samtools/NEWS
+   M /trunk/samtools/bamtk.c
+
+Release samtools-0.1.10 (r829)
+
+------------------------------------------------------------------------
+r828 | lh3lh3 | 2010-11-16 20:48:49 -0500 (Tue, 16 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bamtk.c
+
+update version information: samtools-0.1.9-20 (r828)
+
+------------------------------------------------------------------------
+r827 | lh3lh3 | 2010-11-16 15:32:50 -0500 (Tue, 16 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/call1.c
+
+bcftools: allow to skip indels
+
+------------------------------------------------------------------------
+r826 | lh3lh3 | 2010-11-16 14:11:58 -0500 (Tue, 16 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_md.c
+
+remove ZQ if both BQ and ZQ are present
+
+------------------------------------------------------------------------
+r825 | lh3lh3 | 2010-11-16 13:51:33 -0500 (Tue, 16 Nov 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bam_md.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/samtools.1
+
+ * samtools-0.1.9-18 (r825)
+ * change the behaviour of calmd such that by default it does not change the base quality
+
+------------------------------------------------------------------------
+r824 | lh3lh3 | 2010-11-15 23:31:53 -0500 (Mon, 15 Nov 2010) | 4 lines
+Changed paths:
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/bcftools/call1.c
+   M /trunk/samtools/samtools.1
+
+ * samtools-0.1.9-17 (r824)
+ * added command line options to change the default parameters in indel calling
+ * update the manual
+
+------------------------------------------------------------------------
+r823 | lh3lh3 | 2010-11-15 12:20:13 -0500 (Mon, 15 Nov 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bam_md.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-r823
+ * the BQ tag is now 64 shifted, not 33 shifted
+
+------------------------------------------------------------------------
+r822 | lh3lh3 | 2010-11-15 00:30:18 -0500 (Mon, 15 Nov 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf.h
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/bcftools/vcfutils.pl
+   M /trunk/samtools/misc/samtools.pl
+
+ * samtools-0.1.9-16 (r822)
+ * keep the raw depth because in indel calling, DP4 may be way off the true depth
+
+------------------------------------------------------------------------
+r821 | lh3lh3 | 2010-11-13 01:18:31 -0500 (Sat, 13 Nov 2010) | 4 lines
+Changed paths:
+   M /trunk/samtools/bam_md.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-15 (r821)
+ * calmd: write BQ
+ * skip realignment if BQ is present
+
+------------------------------------------------------------------------
+r820 | lh3lh3 | 2010-11-13 01:08:26 -0500 (Sat, 13 Nov 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-14 (r820)
+ * penalize reads with excessive differences in indel calling
+
+------------------------------------------------------------------------
+r819 | lh3lh3 | 2010-11-12 21:36:27 -0500 (Fri, 12 Nov 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_maqcns.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-13 (r819)
+ * fixed a bug in pileup given refskip
+
+------------------------------------------------------------------------
+r818 | lh3lh3 | 2010-11-12 13:04:53 -0500 (Fri, 12 Nov 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-r818
+ * for indel calling, do two rounds of probabilistic realignments
+
+------------------------------------------------------------------------
+r817 | lh3lh3 | 2010-11-11 20:04:07 -0500 (Thu, 11 Nov 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/bcftools/vcfutils.pl
+
+ * samtools-0.1.19-11 (r817)
+ * only initiate indel calling when 0.2% of reads contain a gap
+
+------------------------------------------------------------------------
+r816 | lh3lh3 | 2010-11-11 01:22:59 -0500 (Thu, 11 Nov 2010) | 7 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf_indel.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.9-10 (r816)
+
+ * I know why the forward method fails. it is because of zero base
+   qualities. when that is fixed, the forward method seems to give
+   better results than Viterbi, as it should be. I am tired...
+
+
+------------------------------------------------------------------------
+r815 | lh3lh3 | 2010-11-11 00:57:15 -0500 (Thu, 11 Nov 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/ChangeLog
+   M /trunk/samtools/bam2bcf_indel.c
+
+effectively revert to the viterbi version. The forward realignment gives too many false positives.
+
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 r814 | lh3lh3 | 2010-11-11 00:18:02 -0500 (Thu, 11 Nov 2010) | 4 lines
 Changed paths: