* samtools-0.1.8-22 (r781)

 * made BAQ the default behavior of mpileup
 * updated manual
 * in merge, force to exit given inconsistent header when "-R" is not in use.

diff --git a/ChangeLog b/ChangeLog
index 6b0ff6cf4e80c0a9a1e989847e86bd1bba9434fe..d46ea253f0660eec473609deb49e1cbda34f269d 100644 (file)
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,1286 @@
+------------------------------------------------------------------------
+r780 | lh3lh3 | 2010-10-27 11:01:11 -0400 (Wed, 27 Oct 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam.h
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.8-21 (r780)
+ * minor speedup to pileup
+
+------------------------------------------------------------------------
+r779 | lh3lh3 | 2010-10-27 09:58:56 -0400 (Wed, 27 Oct 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_pileup.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/examples/toy.sam
+
+improve pileup a little bit
+
+------------------------------------------------------------------------
+r778 | lh3lh3 | 2010-10-27 00:14:43 -0400 (Wed, 27 Oct 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/bam_tview.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.8-20 (r778)
+ * speed up pileup, although I do not know how much is the improvement
+
+------------------------------------------------------------------------
+r777 | lh3lh3 | 2010-10-26 17:26:04 -0400 (Tue, 26 Oct 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/bamtk.c
+   M /trunk/samtools/examples/Makefile
+
+ * samtools-0.1.8-19 (r777)
+ * integrate mpileup features to pileup: min_baseQ, capQ, prob_realn, paired-only and biased prior
+
+------------------------------------------------------------------------
+r776 | lh3lh3 | 2010-10-26 15:27:46 -0400 (Tue, 26 Oct 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_md.c
+
+remove local realignment (probabilistic realignment is still there)
+
+------------------------------------------------------------------------
+r774 | jmarshall | 2010-10-21 06:52:38 -0400 (Thu, 21 Oct 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/sam_view.c
+
+Add the relevant filename or region to error messages, and cause a failure
+exit status where appropriate.  Based on a patch provided by Marcel Martin.
+
+------------------------------------------------------------------------
+r773 | lh3lh3 | 2010-10-19 19:44:31 -0400 (Tue, 19 Oct 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/examples/toy.sam
+   M /trunk/samtools/kaln.c
+
+ * Minor code changes. No real effect.
+ * change quality to 30 in toy.sam
+
+------------------------------------------------------------------------
+r772 | lh3lh3 | 2010-10-18 23:40:13 -0400 (Mon, 18 Oct 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/examples/toy.fa
+   M /trunk/samtools/examples/toy.sam
+
+added another toy example
+
+------------------------------------------------------------------------
+r771 | lh3lh3 | 2010-10-13 23:32:12 -0400 (Wed, 13 Oct 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/call1.c
+   M /trunk/samtools/bcftools/ld.c
+   M /trunk/samtools/bcftools/vcfutils.pl
+
+improve the LD statistics
+
+------------------------------------------------------------------------
+r770 | lh3lh3 | 2010-10-12 23:49:26 -0400 (Tue, 12 Oct 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bcftools/call1.c
+   M /trunk/samtools/bcftools/vcfutils.pl
+
+ * a minor fix to the -L option
+ * add ldstats to vcfutils.pl
+
+------------------------------------------------------------------------
+r769 | lh3lh3 | 2010-10-12 15:51:57 -0400 (Tue, 12 Oct 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/bcf.c
+
+a minor change
+
+------------------------------------------------------------------------
+r768 | lh3lh3 | 2010-10-12 15:49:06 -0400 (Tue, 12 Oct 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/Makefile
+   A /trunk/samtools/bcftools/ld.c
+
+forget to add the key file
+
+------------------------------------------------------------------------
+r767 | lh3lh3 | 2010-10-12 15:48:46 -0400 (Tue, 12 Oct 2010) | 4 lines
+Changed paths:
+   M /trunk/samtools/bcftools/Makefile
+   M /trunk/samtools/bcftools/bcf.c
+   M /trunk/samtools/bcftools/bcf.h
+   M /trunk/samtools/bcftools/call1.c
+   M /trunk/samtools/bcftools/prob1.c
+   M /trunk/samtools/bcftools/vcfutils.pl
+
+ * vcfutils.pl: fixed a typo in help message
+ * added APIs: bcf_append_info() and bcf_cpy()
+ * calculate adjacent LD
+
+------------------------------------------------------------------------
+r766 | lh3lh3 | 2010-10-11 11:06:40 -0400 (Mon, 11 Oct 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/vcfutils.pl
+
+added filter for samtools/bcftools genetated VCFs
+
+------------------------------------------------------------------------
+r765 | lh3lh3 | 2010-10-05 14:05:18 -0400 (Tue, 05 Oct 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bcftools/vcfutils.pl
+   M /trunk/samtools/kaln.c
+
+ * removed a comment line in kaln.c
+ * vcfutils.pl fillac works when GT is not the first field
+
+------------------------------------------------------------------------
+r764 | petulda | 2010-10-05 08:59:36 -0400 (Tue, 05 Oct 2010) | 1 line
+Changed paths:
+   A /trunk/samtools/bcftools/bcf-fix.pl
+
+Convert VCF output of "bcftools view -bgcv" to a valid VCF file
+------------------------------------------------------------------------
+r763 | lh3lh3 | 2010-10-02 22:51:03 -0400 (Sat, 02 Oct 2010) | 4 lines
+Changed paths:
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+   A /trunk/samtools/bcftools/bcftools.1
+   M /trunk/samtools/bcftools/call1.c
+   M /trunk/samtools/samtools.1
+
+ * samtools-0.1.8-18 (r763)
+ * added bcftools manual page
+ * minor fix to mpileup and view command lines
+
+------------------------------------------------------------------------
+r762 | lh3lh3 | 2010-10-02 21:46:25 -0400 (Sat, 02 Oct 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bcftools/bcf.c
+   M /trunk/samtools/bcftools/call1.c
+   M /trunk/samtools/bcftools/vcfutils.pl
+
+ * vcfutils.pl qstats: calculate marginal ts/tv
+ * allow to call genotypes at variant sites
+
+------------------------------------------------------------------------
+r761 | lh3lh3 | 2010-10-01 00:29:55 -0400 (Fri, 01 Oct 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/kaln.c
+   M /trunk/samtools/misc/HmmGlocal.java
+
+I am changing the gap open probability back to 0.001. It seems that
+being conservative here is a good thing...
+
+------------------------------------------------------------------------
+r760 | lh3lh3 | 2010-10-01 00:11:27 -0400 (Fri, 01 Oct 2010) | 5 lines
+Changed paths:
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/kaln.c
+   A /trunk/samtools/misc/HmmGlocal.java
+
+ * samtools-0.1.8-17 (r760)
+ * the default gap open penalty is too small (a typo)
+ * added comments on hmm_realn
+ * Java implementation
+
+------------------------------------------------------------------------
+r759 | lh3lh3 | 2010-09-30 10:12:54 -0400 (Thu, 30 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bamtk.c
+
+mark samtools-0.1.8-16 (r759)
+
+------------------------------------------------------------------------
+r758 | lh3lh3 | 2010-09-30 10:12:02 -0400 (Thu, 30 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/kaln.c
+
+round to the nearest integer
+
+------------------------------------------------------------------------
+r757 | lh3lh3 | 2010-09-28 17:16:43 -0400 (Tue, 28 Sep 2010) | 4 lines
+Changed paths:
+   M /trunk/samtools/kaln.c
+
+I was trying to accelerate ka_prob_glocal() as this will be the
+bottleneck. After an hour, the only gain is to change division to
+multiplication. OK. I will stop.
+
+------------------------------------------------------------------------
+r756 | lh3lh3 | 2010-09-28 16:57:49 -0400 (Tue, 28 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/kaln.c
+
+this is interesting. multiplication is much faster than division, at least on my Mac
+
+------------------------------------------------------------------------
+r755 | lh3lh3 | 2010-09-28 16:19:13 -0400 (Tue, 28 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/kaln.c
+
+minor changes
+
+------------------------------------------------------------------------
+r754 | lh3lh3 | 2010-09-28 15:44:16 -0400 (Tue, 28 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_md.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/kaln.c
+
+prob_realn() seems working!
+
+------------------------------------------------------------------------
+r753 | lh3lh3 | 2010-09-28 12:48:23 -0400 (Tue, 28 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/kaln.c
+
+minor
+
+------------------------------------------------------------------------
+r752 | lh3lh3 | 2010-09-28 12:47:41 -0400 (Tue, 28 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/kaln.c
+   M /trunk/samtools/kaln.h
+
+Convert phredQ to probabilities
+
+------------------------------------------------------------------------
+r751 | lh3lh3 | 2010-09-28 12:32:08 -0400 (Tue, 28 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/kaln.c
+   M /trunk/samtools/kaln.h
+
+Implement the glocal HMM; discard the extention HMM
+
+------------------------------------------------------------------------
+r750 | lh3lh3 | 2010-09-28 00:06:11 -0400 (Tue, 28 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/kaln.c
+
+improve numerical stability
+
+------------------------------------------------------------------------
+r749 | lh3lh3 | 2010-09-27 23:27:54 -0400 (Mon, 27 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/kaln.c
+
+more comments
+
+------------------------------------------------------------------------
+r748 | lh3lh3 | 2010-09-27 23:17:16 -0400 (Mon, 27 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/kaln.c
+
+fixed a bug in banded DP
+
+------------------------------------------------------------------------
+r747 | lh3lh3 | 2010-09-27 23:05:12 -0400 (Mon, 27 Sep 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/kaln.c
+
+ * fixed that weird issue.
+ * the banded version is NOT working
+
+------------------------------------------------------------------------
+r746 | lh3lh3 | 2010-09-27 22:57:05 -0400 (Mon, 27 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/kaln.c
+
+More comments. This version seems working, but something is a little weird...
+
+------------------------------------------------------------------------
+r745 | lh3lh3 | 2010-09-27 17:21:40 -0400 (Mon, 27 Sep 2010) | 6 lines
+Changed paths:
+   M /trunk/samtools/kaln.c
+
+A little code cleanup. Now the forward and backback algorithms give
+nearly identical P(x), which means both are close to the correct
+forms. However, I have only tested on toy examples. Minor errors in
+the implementation may not be obvious.
+
+
+------------------------------------------------------------------------
+r744 | lh3lh3 | 2010-09-27 16:55:15 -0400 (Mon, 27 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bam_sort.c
+   M /trunk/samtools/kaln.c
+   M /trunk/samtools/kaln.h
+
+...
+
+------------------------------------------------------------------------
+r743 | jmarshall | 2010-09-27 08:19:06 -0400 (Mon, 27 Sep 2010) | 6 lines
+Changed paths:
+   M /trunk/samtools/bam_sort.c
+
+Abort if merge -h's INH.SAM cannot be opened, just as we abort
+if any of the IN#.BAM input files cannot be opened.
+
+Also propagate any error indication returned by bam_merge_core()
+to samtools merge's exit status.
+
+------------------------------------------------------------------------
+r741 | jmarshall | 2010-09-24 11:08:24 -0400 (Fri, 24 Sep 2010) | 5 lines
+Changed paths:
+   M /trunk/samtools/bam_index.c
+
+Use bam_validate1() to detect garbage records in the event of a corrupt
+BAI index file that causes a bam_seek() to an invalid position.  At most
+one record (namely, the bam_iter_read terminator) is tested per bam_fetch()
+call, so the cost is insignificant in the normal case.
+
+------------------------------------------------------------------------
+r740 | jmarshall | 2010-09-24 11:00:19 -0400 (Fri, 24 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam.c
+   M /trunk/samtools/bam.h
+
+Add bam_validate1().
+
+------------------------------------------------------------------------
+r739 | lh3lh3 | 2010-09-22 12:07:50 -0400 (Wed, 22 Sep 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_md.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.8-15 (r379)
+ * allow to change capQ parameter in calmd
+
+------------------------------------------------------------------------
+r738 | jmarshall | 2010-09-22 11:15:33 -0400 (Wed, 22 Sep 2010) | 13 lines
+Changed paths:
+   M /trunk/samtools/bam_index.c
+   M /trunk/samtools/sam_view.c
+
+When bam_read1() returns an error (return value <= -2), propagate that error
+to bam_iter_read()'s own return value.  Similarly, also propagate it up to
+bam_fetch()'s return value.  Previously bam_fetch() always returned 0, and
+callers ignored its return value anyway.  With this change, 0 continues to
+indicate success, while <= -2 (which can be written as < 0, as -1 is never
+returned) indicates corrupted input.
+
+bam_iter_read() ought also to propagate errors returned by bam_seek().
+
+main_samview() can now print an error message and fail when bam_fetch()
+detects that a .bai index file is corrupted or otherwise does not correspond
+to the .bam file it is being used with.
+
+------------------------------------------------------------------------
+r737 | jmarshall | 2010-09-22 10:47:42 -0400 (Wed, 22 Sep 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_index.c
+
+0 is a successful return value from bam_read1().  (In practice, it never
+returns 0 anyway; but all the other callers treat 0 as successful.)
+
+------------------------------------------------------------------------
+r736 | lh3lh3 | 2010-09-20 17:43:08 -0400 (Mon, 20 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam.h
+   M /trunk/samtools/bam_index.c
+   M /trunk/samtools/bam_sort.c
+
+ * merge files region-by-region. work on small examples but more tests are needed.
+
+------------------------------------------------------------------------
+r735 | lh3lh3 | 2010-09-20 16:56:24 -0400 (Mon, 20 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/vcfutils.pl
+
+improve qstats by checking the alleles as well
+
+------------------------------------------------------------------------
+r734 | lh3lh3 | 2010-09-17 18:12:13 -0400 (Fri, 17 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/vcfutils.pl
+
+convert UCSC SNP SQL dump to VCF
+
+------------------------------------------------------------------------
+r733 | lh3lh3 | 2010-09-17 13:02:11 -0400 (Fri, 17 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/vcfutils.pl
+
+hapmap2vcf convertor
+
+------------------------------------------------------------------------
+r732 | lh3lh3 | 2010-09-17 10:11:37 -0400 (Fri, 17 Sep 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bcftools/Makefile
+   M /trunk/samtools/bcftools/bcf.c
+   M /trunk/samtools/bcftools/bcf.h
+   M /trunk/samtools/bcftools/vcf.c
+
+ * added comments
+ * VCF->BCF is not possible without knowing the sequence dictionary before hand...
+
+------------------------------------------------------------------------
+r731 | lh3lh3 | 2010-09-17 09:15:53 -0400 (Fri, 17 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bcftools/bcf.c
+   M /trunk/samtools/bcftools/bcf.h
+   M /trunk/samtools/bcftools/bcfutils.c
+   M /trunk/samtools/bcftools/call1.c
+   M /trunk/samtools/bcftools/vcf.c
+
+ * put n_smpl to "bcf1_t" to simplify API a little
+
+------------------------------------------------------------------------
+r730 | lh3lh3 | 2010-09-16 21:36:01 -0400 (Thu, 16 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/bcf.h
+   M /trunk/samtools/bcftools/call1.c
+   M /trunk/samtools/bcftools/index.c
+
+fixed a bug in indexing
+
+------------------------------------------------------------------------
+r729 | lh3lh3 | 2010-09-16 16:54:48 -0400 (Thu, 16 Sep 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam.c
+   M /trunk/samtools/bam_md.c
+   M /trunk/samtools/bam_pileup.c
+
+ * fixed a bug in capQ
+ * valgrind identifies a use of uninitialised value, but I have not fixed it.
+
+------------------------------------------------------------------------
+r728 | lh3lh3 | 2010-09-16 15:03:59 -0400 (Thu, 16 Sep 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bgzip.c
+   M /trunk/samtools/razip.c
+
+ * fixed a bug in razip: -c will delete the input file
+ * copy tabix/bgzip to here
+
+------------------------------------------------------------------------
+r727 | lh3lh3 | 2010-09-16 13:45:49 -0400 (Thu, 16 Sep 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_md.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.8-14 (r727)
+ * allow to change the capQ parameter at the command line
+
+------------------------------------------------------------------------
+r726 | lh3lh3 | 2010-09-16 13:38:43 -0400 (Thu, 16 Sep 2010) | 4 lines
+Changed paths:
+   M /trunk/samtools/bam_md.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bcftools/vcfutils.pl
+   M /trunk/samtools/misc/samtools.pl
+
+ * added varFilter to vcfutils.pl
+ * reimplement realn(). now it performs a local alignment
+ * added cap_mapQ() to cap mapping quality when there are many substitutions
+
+------------------------------------------------------------------------
+r724 | lh3lh3 | 2010-09-15 00:18:31 -0400 (Wed, 15 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/Makefile
+   A /trunk/samtools/bcftools/bcf2qcall.c
+   M /trunk/samtools/bcftools/call1.c
+
+ * convert BCF to QCALL input
+
+------------------------------------------------------------------------
+r723 | lh3lh3 | 2010-09-14 22:41:50 -0400 (Tue, 14 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_md.c
+
+dynamic band width in realignment
+
+------------------------------------------------------------------------
+r722 | lh3lh3 | 2010-09-14 22:05:32 -0400 (Tue, 14 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_md.c
+   M /trunk/samtools/bam_plcmd.c
+
+fixed a bug in realignment
+
+------------------------------------------------------------------------
+r721 | lh3lh3 | 2010-09-14 20:54:09 -0400 (Tue, 14 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/prob1.c
+
+fixed a minor issue
+
+------------------------------------------------------------------------
+r720 | lh3lh3 | 2010-09-14 19:25:10 -0400 (Tue, 14 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+   M /trunk/samtools/bam_maqcns.c
+   M /trunk/samtools/bam_md.c
+
+fixed a bug in realignment
+
+------------------------------------------------------------------------
+r719 | lh3lh3 | 2010-09-14 19:18:24 -0400 (Tue, 14 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_plcmd.c
+
+minor changes. It is BUGGY now!
+
+------------------------------------------------------------------------
+r718 | lh3lh3 | 2010-09-14 16:32:33 -0400 (Tue, 14 Sep 2010) | 4 lines
+Changed paths:
+   M /trunk/samtools/bam_md.c
+   M /trunk/samtools/bam_pileup.c
+   M /trunk/samtools/kaln.c
+   M /trunk/samtools/kaln.h
+
+ * aggressive gapped aligner is implemented in calmd.
+ * distinguish gap_open and gap_end_open in banded alignment
+ * make tview accepts alignment with heading and tailing D
+
+------------------------------------------------------------------------
+r717 | jmarshall | 2010-09-14 09:04:28 -0400 (Tue, 14 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools
+
+Add svn:ignore properties for generated files that don't appear in "make all".
+
+------------------------------------------------------------------------
+r716 | jmarshall | 2010-09-13 08:37:53 -0400 (Mon, 13 Sep 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools
+   M /trunk/samtools/bcftools
+   M /trunk/samtools/misc
+
+Add svn:ignore properties listing the generated files.
+(Except for *.o, which we'll assume is in global-ignores.)
+
+------------------------------------------------------------------------
+r715 | lh3lh3 | 2010-09-08 12:53:55 -0400 (Wed, 08 Sep 2010) | 5 lines
+Changed paths:
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/bcftools/call1.c
+   M /trunk/samtools/bcftools/prob1.c
+   M /trunk/samtools/sample.c
+   M /trunk/samtools/sample.h
+
+ * samtools-0.1.8-13 (r715)
+ * fixed a bug in identifying SM across files
+ * bcftools: estimate heterozygosity
+ * bcftools: allow to skip sites without reference bases
+
+------------------------------------------------------------------------
+r713 | lh3lh3 | 2010-09-03 17:19:12 -0400 (Fri, 03 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/Makefile
+   M /trunk/samtools/bcftools/call1.c
+   M /trunk/samtools/bcftools/prob1.c
+   M /trunk/samtools/bcftools/prob1.h
+
+quite a lot changes to the contrast caller, but I still feel something is missing...
+
+------------------------------------------------------------------------
+r711 | lh3lh3 | 2010-09-03 00:30:48 -0400 (Fri, 03 Sep 2010) | 4 lines
+Changed paths:
+   M /trunk/samtools/bcftools/Makefile
+   M /trunk/samtools/bcftools/call1.c
+   M /trunk/samtools/bcftools/prob1.c
+   M /trunk/samtools/bcftools/vcfutils.pl
+
+ * changed 3.434 to 4.343 (typo!)
+ * fixed a bug in the contrast caller
+ * calculate heterozygosity
+
+------------------------------------------------------------------------
+r710 | lh3lh3 | 2010-09-01 23:24:47 -0400 (Wed, 01 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/bcf.h
+   M /trunk/samtools/bcftools/bcfutils.c
+   M /trunk/samtools/bcftools/call1.c
+
+SNP calling from the GL field
+
+------------------------------------------------------------------------
+r709 | lh3lh3 | 2010-09-01 18:52:30 -0400 (Wed, 01 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/vcf.c
+
+fixed another problem
+
+------------------------------------------------------------------------
+r708 | lh3lh3 | 2010-09-01 18:31:17 -0400 (Wed, 01 Sep 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bcftools/bcf.c
+   M /trunk/samtools/bcftools/vcf.c
+
+ * fixed bugs in parsing VCF
+ * parser now works with GT/GQ/DP/PL/GL
+
+------------------------------------------------------------------------
+r707 | lh3lh3 | 2010-09-01 15:28:29 -0400 (Wed, 01 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/Makefile
+   M /trunk/samtools/bcftools/prob1.c
+
+Do not compile _BCF_QUAD by default
+
+------------------------------------------------------------------------
+r706 | lh3lh3 | 2010-09-01 15:21:41 -0400 (Wed, 01 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/bcf.c
+   M /trunk/samtools/bcftools/bcf.h
+   M /trunk/samtools/bcftools/bcfutils.c
+   M /trunk/samtools/bcftools/call1.c
+
+Write the correct ALT and PL in the SNP calling mode.
+
+------------------------------------------------------------------------
+r705 | lh3lh3 | 2010-09-01 12:50:33 -0400 (Wed, 01 Sep 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/vcfutils.pl
+
+more commands for my own uses
+
+------------------------------------------------------------------------
+r704 | lh3lh3 | 2010-09-01 09:26:10 -0400 (Wed, 01 Sep 2010) | 2 lines
+Changed paths:
+   A /trunk/samtools/bcftools/vcfutils.pl
+
+Utilities for processing VCF
+
+------------------------------------------------------------------------
+r703 | lh3lh3 | 2010-08-31 16:44:57 -0400 (Tue, 31 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/Makefile
+   M /trunk/samtools/bcftools/call1.c
+   M /trunk/samtools/bcftools/prob1.c
+   M /trunk/samtools/bcftools/prob1.h
+
+preliminary contrast variant caller
+
+------------------------------------------------------------------------
+r702 | lh3lh3 | 2010-08-31 12:28:39 -0400 (Tue, 31 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/call1.c
+   M /trunk/samtools/bcftools/prob1.c
+   M /trunk/samtools/bcftools/prob1.h
+
+z' and z'' can be calculated
+
+------------------------------------------------------------------------
+r701 | lh3lh3 | 2010-08-31 10:20:57 -0400 (Tue, 31 Aug 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bcftools/Makefile
+   A /trunk/samtools/bcftools/call1.c (from /trunk/samtools/bcftools/vcfout.c:699)
+   M /trunk/samtools/bcftools/prob1.c
+   D /trunk/samtools/bcftools/vcfout.c
+
+ * rename vcfout.c as call1.c
+ * prepare to add two-sample comparison
+
+------------------------------------------------------------------------
+r699 | lh3lh3 | 2010-08-24 15:28:16 -0400 (Tue, 24 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/vcfout.c
+
+fixed a bug in calculating the t statistics
+
+------------------------------------------------------------------------
+r698 | lh3lh3 | 2010-08-24 14:05:50 -0400 (Tue, 24 Aug 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf.h
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/bcftools/kfunc.c
+   M /trunk/samtools/bcftools/vcfout.c
+
+ * samtools-0.1.8-13 (r698)
+ * perform one-tailed t-test for baseQ, mapQ and endDist
+
+------------------------------------------------------------------------
+r697 | lh3lh3 | 2010-08-24 12:30:13 -0400 (Tue, 24 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/kfunc.c
+
+added regularized incomplete beta function
+
+------------------------------------------------------------------------
+r695 | lh3lh3 | 2010-08-23 17:36:17 -0400 (Mon, 23 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_maqcns.c
+   M /trunk/samtools/bam_plcmd.c
+
+change the default correlation coefficient
+
+------------------------------------------------------------------------
+r694 | lh3lh3 | 2010-08-23 14:46:52 -0400 (Mon, 23 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/bcf.c
+   M /trunk/samtools/bcftools/vcfout.c
+
+print QUAL as floating numbers
+
+------------------------------------------------------------------------
+r693 | lh3lh3 | 2010-08-23 14:06:07 -0400 (Mon, 23 Aug 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/examples/Makefile
+   A /trunk/samtools/sample.c
+   A /trunk/samtools/sample.h
+
+ * samtools-0.1.8-12 (r692)
+ * group data by samples in "mpileup -g"
+
+------------------------------------------------------------------------
+r692 | lh3lh3 | 2010-08-23 10:58:53 -0400 (Mon, 23 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+   D /trunk/samtools/bam_mcns.c
+   D /trunk/samtools/bam_mcns.h
+   M /trunk/samtools/bam_plcmd.c
+
+remove VCF output in mpileup
+
+------------------------------------------------------------------------
+r691 | lh3lh3 | 2010-08-23 10:48:20 -0400 (Mon, 23 Aug 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf.h
+
+ * use the revised MAQ error model for mpileup
+ * prepare to remove the independent model from mpileup
+
+------------------------------------------------------------------------
+r690 | lh3lh3 | 2010-08-20 15:46:40 -0400 (Fri, 20 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+   M /trunk/samtools/bam_maqcns.c
+   M /trunk/samtools/bam_maqcns.h
+   M /trunk/samtools/bam_plcmd.c
+   A /trunk/samtools/errmod.c
+   A /trunk/samtools/errmod.h
+   M /trunk/samtools/ksort.h
+
+added revised MAQ error model
+
+------------------------------------------------------------------------
+r689 | lh3lh3 | 2010-08-18 09:55:20 -0400 (Wed, 18 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/prob1.c
+   M /trunk/samtools/bcftools/prob1.h
+   M /trunk/samtools/bcftools/vcfout.c
+
+allow to read the prior from the error output. EM iteration is working.
+
+------------------------------------------------------------------------
+r688 | lh3lh3 | 2010-08-17 12:12:20 -0400 (Tue, 17 Aug 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bcftools/main.c
+   M /trunk/samtools/bcftools/vcf.c
+
+ * write a little more VCF header
+ * concatenate BCFs
+
+------------------------------------------------------------------------
+r687 | lh3lh3 | 2010-08-16 20:53:16 -0400 (Mon, 16 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/bcf.c
+   M /trunk/samtools/bcftools/bcf.h
+   M /trunk/samtools/bcftools/bcf.tex
+
+use float for QUAL
+
+------------------------------------------------------------------------
+r686 | lh3lh3 | 2010-08-14 00:11:13 -0400 (Sat, 14 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/bcf.c
+   M /trunk/samtools/bcftools/prob1.c
+
+faster for large sample size (in principle)
+
+------------------------------------------------------------------------
+r685 | lh3lh3 | 2010-08-13 23:28:31 -0400 (Fri, 13 Aug 2010) | 4 lines
+Changed paths:
+   M /trunk/samtools/bcftools/prob1.c
+
+ * a numerically stable method to calculate z_{jk}
+ * currently slower than the old method but will be important for large sample size
+ * in principle, we can speed up for large n, but have not tried
+
+------------------------------------------------------------------------
+r684 | lh3lh3 | 2010-08-11 21:58:31 -0400 (Wed, 11 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/vcfout.c
+
+fixed an issue in parsing integer
+
+------------------------------------------------------------------------
+r683 | lh3lh3 | 2010-08-09 13:05:07 -0400 (Mon, 09 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/bcf.c
+
+do not print refname if file is converted from VCF
+
+------------------------------------------------------------------------
+r682 | lh3lh3 | 2010-08-09 12:59:47 -0400 (Mon, 09 Aug 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bcftools/vcf.c
+
+ * parse PL
+ * fixed a bug in parsing VCF
+
+------------------------------------------------------------------------
+r681 | lh3lh3 | 2010-08-09 12:49:23 -0400 (Mon, 09 Aug 2010) | 4 lines
+Changed paths:
+   M /trunk/samtools/bcftools/bcf.c
+   M /trunk/samtools/bcftools/bcf.h
+   M /trunk/samtools/bcftools/bcfutils.c
+   M /trunk/samtools/bcftools/main.c
+   M /trunk/samtools/bcftools/vcf.c
+   M /trunk/samtools/bcftools/vcfout.c
+   M /trunk/samtools/bgzf.c
+   M /trunk/samtools/kstring.c
+
+ * fixed a bug in kstrtok@kstring.c
+ * preliminary VCF parser (not parse everything for now)
+ * improved view interface
+
+------------------------------------------------------------------------
+r680 | lh3lh3 | 2010-08-09 10:43:13 -0400 (Mon, 09 Aug 2010) | 4 lines
+Changed paths:
+   M /trunk/samtools/bcftools/bcf.c
+   M /trunk/samtools/bcftools/bcf.h
+   M /trunk/samtools/bcftools/vcfout.c
+   M /trunk/samtools/kstring.c
+   M /trunk/samtools/kstring.h
+
+ * improved kstring (added kstrtok)
+ * removed the limit on the format string length in bcftools
+ * use kstrtok to parse format which fixed a bug in the old code
+
+------------------------------------------------------------------------
+r679 | lh3lh3 | 2010-08-09 01:12:05 -0400 (Mon, 09 Aug 2010) | 2 lines
+Changed paths:
+   A /trunk/samtools/bcftools/README
+   M /trunk/samtools/bcftools/vcfout.c
+
+help messages
+
+------------------------------------------------------------------------
+r678 | lh3lh3 | 2010-08-09 00:01:52 -0400 (Mon, 09 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/vcfout.c
+
+perform single-tail test for ED4
+
+------------------------------------------------------------------------
+r677 | lh3lh3 | 2010-08-08 23:48:35 -0400 (Sun, 08 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/Makefile
+   M /trunk/samtools/bcftools/kfunc.c
+   M /trunk/samtools/bcftools/vcfout.c
+
+ * test depth, end distance and HWE
+
+------------------------------------------------------------------------
+r676 | lh3lh3 | 2010-08-08 02:04:15 -0400 (Sun, 08 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/kfunc.c
+
+reimplement incomplete gamma functions. no copy-paste
+
+------------------------------------------------------------------------
+r675 | lh3lh3 | 2010-08-06 22:42:54 -0400 (Fri, 06 Aug 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf.h
+   M /trunk/samtools/bcftools/fet.c
+   M /trunk/samtools/bcftools/prob1.c
+   M /trunk/samtools/bcftools/prob1.h
+   M /trunk/samtools/bcftools/vcfout.c
+
+ * bcftools: add HWE (no testing for now)
+ * record end dist in a 2x2 table, not avg, std any more
+
+------------------------------------------------------------------------
+r674 | lh3lh3 | 2010-08-06 17:30:16 -0400 (Fri, 06 Aug 2010) | 3 lines
+Changed paths:
+   A /trunk/samtools/bcftools/kfunc.c
+
+ * Special functions: log(gamma()), erfc(), P(a,x) (incomplete gamma)
+ * Not using Numerical Recipe due to licensing issues
+
+------------------------------------------------------------------------
+r673 | lh3lh3 | 2010-08-05 23:46:53 -0400 (Thu, 05 Aug 2010) | 2 lines
+Changed paths:
+   A /trunk/samtools/bcftools/fet.c
+
+Fisher's exact test
+
+------------------------------------------------------------------------
+r672 | lh3lh3 | 2010-08-05 21:48:33 -0400 (Thu, 05 Aug 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf.h
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/examples/Makefile
+
+ * samtools-0.1.8-11 (r672)
+ * collect more stats for allele balance test in bcftools (not yet)
+
+------------------------------------------------------------------------
+r671 | lh3lh3 | 2010-08-05 16:17:58 -0400 (Thu, 05 Aug 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bcftools/bcf.c
+   M /trunk/samtools/bcftools/main.c
+
+ * the code base is stablized again.
+ * I will delay the vcf parser, which is quite complicated but with little value for now
+
+------------------------------------------------------------------------
+r670 | lh3lh3 | 2010-08-05 16:03:23 -0400 (Thu, 05 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/examples/Makefile
+
+minor
+
+------------------------------------------------------------------------
+r669 | lh3lh3 | 2010-08-05 16:03:08 -0400 (Thu, 05 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcftools/vcf.c
+
+unfinished vcf parser
+
+------------------------------------------------------------------------
+r668 | lh3lh3 | 2010-08-05 15:46:40 -0400 (Thu, 05 Aug 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bcftools/Makefile
+   M /trunk/samtools/bcftools/bcf.c
+   M /trunk/samtools/bcftools/bcf.h
+   M /trunk/samtools/bcftools/bcfutils.c
+   M /trunk/samtools/bcftools/index.c
+   M /trunk/samtools/bcftools/main.c
+   A /trunk/samtools/bcftools/vcf.c
+   M /trunk/samtools/bcftools/vcfout.c
+
+ * added prelimiary VCF parser (not finished)
+ * change struct a bit
+
+------------------------------------------------------------------------
+r667 | lh3lh3 | 2010-08-03 22:35:27 -0400 (Tue, 03 Aug 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf.h
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bcftools/bcf.c
+
+ * allow to set min base q
+ * fixed a bug in mpileup -u
+
+------------------------------------------------------------------------
+r666 | lh3lh3 | 2010-08-03 22:08:44 -0400 (Tue, 03 Aug 2010) | 2 lines
+Changed paths:
+   A /trunk/samtools/bcftools/bcf.tex
+
+spec
+
+------------------------------------------------------------------------
+r665 | lh3lh3 | 2010-08-03 21:18:57 -0400 (Tue, 03 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/examples/Makefile
+
+added more examples
+
+------------------------------------------------------------------------
+r664 | lh3lh3 | 2010-08-03 21:13:00 -0400 (Tue, 03 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf.h
+   M /trunk/samtools/bcftools/Makefile
+
+fixed compilation error
+
+------------------------------------------------------------------------
+r662 | lh3lh3 | 2010-08-03 21:04:00 -0400 (Tue, 03 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+   D /trunk/samtools/bcf.c
+   D /trunk/samtools/bcf.h
+   A /trunk/samtools/bcftools
+   A /trunk/samtools/bcftools/Makefile
+   A /trunk/samtools/bcftools/bcf.c
+   A /trunk/samtools/bcftools/bcf.h
+   A /trunk/samtools/bcftools/bcfutils.c
+   A /trunk/samtools/bcftools/index.c
+   A /trunk/samtools/bcftools/main.c
+   A /trunk/samtools/bcftools/prob1.c
+   A /trunk/samtools/bcftools/prob1.h
+   A /trunk/samtools/bcftools/vcfout.c
+
+move bcftools to samtools
+
+------------------------------------------------------------------------
+r660 | lh3lh3 | 2010-08-03 15:58:32 -0400 (Tue, 03 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+
+fixed another minor bug
+
+------------------------------------------------------------------------
+r658 | lh3lh3 | 2010-08-03 15:06:45 -0400 (Tue, 03 Aug 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/bcf.c
+
+ * samtools-0.1.8-10 (r658)
+ * fixed a bug in bam2bcf when the reference is N
+
+------------------------------------------------------------------------
+r657 | lh3lh3 | 2010-08-03 14:50:23 -0400 (Tue, 03 Aug 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf.h
+
+ * fixed a bug
+ * treat ambiguous ref base as the fifth base
+
+------------------------------------------------------------------------
+r654 | lh3lh3 | 2010-08-02 17:38:27 -0400 (Mon, 02 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/bcftools/bcf.c
+   M /trunk/samtools/bcf.c
+
+missing a column in VCF output...
+
+------------------------------------------------------------------------
+r653 | lh3lh3 | 2010-08-02 17:31:33 -0400 (Mon, 02 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcf.c
+
+fixed a memory leak
+
+------------------------------------------------------------------------
+r651 | lh3lh3 | 2010-08-02 17:27:31 -0400 (Mon, 02 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bcf.c
+
+fixed a bug in bcf reader
+
+------------------------------------------------------------------------
+r650 | lh3lh3 | 2010-08-02 17:00:41 -0400 (Mon, 02 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam2bcf.c
+
+fixed a bug
+
+------------------------------------------------------------------------
+r649 | lh3lh3 | 2010-08-02 16:49:35 -0400 (Mon, 02 Aug 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+   M /trunk/samtools/bam2bcf.c
+   M /trunk/samtools/bam2bcf.h
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.8-9 (r649)
+ * lossless representation of PL in BCF output
+
+------------------------------------------------------------------------
+r648 | lh3lh3 | 2010-08-02 16:07:25 -0400 (Mon, 02 Aug 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+   A /trunk/samtools/bam2bcf.c
+   A /trunk/samtools/bam2bcf.h
+   M /trunk/samtools/bam_plcmd.c
+   A /trunk/samtools/bcf.c
+   A /trunk/samtools/bcf.h
+
+Generate binary VCF
+
+------------------------------------------------------------------------
+r644 | lh3lh3 | 2010-07-28 11:59:19 -0400 (Wed, 28 Jul 2010) | 5 lines
+Changed paths:
+   M /trunk/samtools/bam_mcns.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.8-8 (r644)
+ * mpileup becomes a little stable again
+ * the method is slightly different, but is more theoretically correct
+ * snp calling is O(n^2) instead of O(n^3)
+
+------------------------------------------------------------------------
+r643 | lh3lh3 | 2010-07-28 11:54:15 -0400 (Wed, 28 Jul 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_mcns.c
+
+ * fixed a STUPID bug, which cost me a lot of time.
+ * I am going to clean up mcns a little bit
+
+------------------------------------------------------------------------
+r642 | lh3lh3 | 2010-07-27 23:23:07 -0400 (Tue, 27 Jul 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_mcns.c
+   M /trunk/samtools/bam_mcns.h
+   M /trunk/samtools/bam_plcmd.c
+
+supposedly this is THE correct implementation, but more testing is needed
+
+------------------------------------------------------------------------
+r641 | lh3lh3 | 2010-07-27 22:43:39 -0400 (Tue, 27 Jul 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_mcns.c
+
+NOT ready yet. Going to make further changes...
+
+------------------------------------------------------------------------
+r639 | lh3lh3 | 2010-07-25 22:18:38 -0400 (Sun, 25 Jul 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_mcns.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.8-7 (r639)
+ * fixed the reference allele assignment
+
+------------------------------------------------------------------------
+r638 | lh3lh3 | 2010-07-25 12:01:26 -0400 (Sun, 25 Jul 2010) | 5 lines
+Changed paths:
+   M /trunk/samtools/bam_mcns.c
+   M /trunk/samtools/bam_mcns.h
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.8-6 (r638)
+ * skip isnan/isinf in case of float underflow
+ * added the flat prior
+ * fixed an issue where there are no reads supporting the reference
+
+------------------------------------------------------------------------
+r637 | lh3lh3 | 2010-07-24 14:16:27 -0400 (Sat, 24 Jul 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_plcmd.c
+
+minor changes
+
+------------------------------------------------------------------------
+r636 | lh3lh3 | 2010-07-24 14:07:27 -0400 (Sat, 24 Jul 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_mcns.c
+   M /trunk/samtools/bam_mcns.h
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+
+minor tweaks
+
+------------------------------------------------------------------------
+r635 | lh3lh3 | 2010-07-24 01:49:49 -0400 (Sat, 24 Jul 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_mcns.c
+   M /trunk/samtools/bam_mcns.h
+   M /trunk/samtools/bam_plcmd.c
+
+posterior expectation FINALLY working. I am so tired...
+
+------------------------------------------------------------------------
+r633 | lh3lh3 | 2010-07-23 13:50:48 -0400 (Fri, 23 Jul 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_plcmd.c
+
+another minor fix to mpileup
+
+------------------------------------------------------------------------
+r632 | lh3lh3 | 2010-07-23 13:43:31 -0400 (Fri, 23 Jul 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_plcmd.c
+
+added the format column
+
+------------------------------------------------------------------------
+r631 | lh3lh3 | 2010-07-23 13:25:44 -0400 (Fri, 23 Jul 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_mcns.c
+   M /trunk/samtools/bam_mcns.h
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+
+added an alternative prior
+
+------------------------------------------------------------------------
+r628 | lh3lh3 | 2010-07-23 11:48:51 -0400 (Fri, 23 Jul 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/bam_mcns.c
+   M /trunk/samtools/bam_mcns.h
+   M /trunk/samtools/bam_plcmd.c
+
+calculate posterior allele frequency
+
+------------------------------------------------------------------------
+r627 | lh3lh3 | 2010-07-22 21:39:13 -0400 (Thu, 22 Jul 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_mcns.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.8-3 (r627)
+ * multi-sample snp calling appears to work. More tests needed.
+
+------------------------------------------------------------------------
+r626 | lh3lh3 | 2010-07-22 16:37:56 -0400 (Thu, 22 Jul 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_mcns.c
+   M /trunk/samtools/bam_mcns.h
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bam_tview.c
+
+ * preliminary multisample SNP caller.
+ * something looks not so right, but it largely works
+
+------------------------------------------------------------------------
+r617 | lh3lh3 | 2010-07-14 16:26:27 -0400 (Wed, 14 Jul 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_mcns.c
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+
+ * samtools-0.1.8-2 (r617)
+ * allele frequency calculation apparently works...
+
+------------------------------------------------------------------------
+r616 | lh3lh3 | 2010-07-14 13:33:51 -0400 (Wed, 14 Jul 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/Makefile
+   A /trunk/samtools/bam_mcns.c
+   A /trunk/samtools/bam_mcns.h
+   M /trunk/samtools/bam_plcmd.c
+
+ * added mutli-sample framework. It is not working, yet.
+ * improved the mpileup interface
+
+------------------------------------------------------------------------
+r615 | lh3lh3 | 2010-07-13 14:50:12 -0400 (Tue, 13 Jul 2010) | 3 lines
+Changed paths:
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/misc/Makefile
+
+ * samtools-0.1.8-1 (r615)
+ * allow to get mpileup at required sites
+
+------------------------------------------------------------------------
+r613 | lh3lh3 | 2010-07-11 22:40:56 -0400 (Sun, 11 Jul 2010) | 2 lines
+Changed paths:
+   M /trunk/samtools/ChangeLog
+   M /trunk/samtools/NEWS
+   M /trunk/samtools/bam_plcmd.c
+   M /trunk/samtools/bamtk.c
+   M /trunk/samtools/samtools.1
+
+Release samtools-0.1.8
+

 ------------------------------------------------------------------------
 r612 | lh3lh3 | 2010-07-11 21:08:56 -0400 (Sun, 11 Jul 2010) | 2 lines
 Changed paths:
 ------------------------------------------------------------------------
 r612 | lh3lh3 | 2010-07-11 21:08:56 -0400 (Sun, 11 Jul 2010) | 2 lines
 Changed paths:

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 6d42471c007a6b34d5b7b1db3ee535c974564839..23602ccd5bcf6dc116632fa1bdb9483993aebf92 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -768,7 +768,8 @@ int bam_mpileup(int argc, char *argv[])
        mplp.max_mq = 60;
        mplp.min_baseQ = 13;
        mplp.capQ_thres = 0;
        mplp.max_mq = 60;
        mplp.min_baseQ = 13;
        mplp.capQ_thres = 0;

-       while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:")) >= 0) {
+       mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
+       while ((c = getopt(argc, argv, "gf:r:l:M:q:Q:uaORC:B")) >= 0) {

                switch (c) {
                case 'f':
                        mplp.fai = fai_load(optarg);
                switch (c) {
                case 'f':
                        mplp.fai = fai_load(optarg);


@@ -779,6 +780,7 @@ int bam_mpileup(int argc, char *argv[])
                case 'g': mplp.flag |= MPLP_GLF; break;
                case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break;
                case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break;
                case 'g': mplp.flag |= MPLP_GLF; break;
                case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break;
                case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break;

+               case 'B': mplp.flag &= ~MPLP_REALN & ~MPLP_NO_ORPHAN; break;

                case 'O': mplp.flag |= MPLP_NO_ORPHAN; break;
                case 'R': mplp.flag |= MPLP_REALN; break;
                case 'C': mplp.capQ_thres = atoi(optarg); break;
                case 'O': mplp.flag |= MPLP_NO_ORPHAN; break;
                case 'R': mplp.flag |= MPLP_REALN; break;
                case 'C': mplp.capQ_thres = atoi(optarg); break;


@@ -798,6 +800,7 @@ int bam_mpileup(int argc, char *argv[])
                fprintf(stderr, "         -q INT      filter out alignment with MQ smaller than INT [%d]\n", mplp.min_mq);
                fprintf(stderr, "         -g          generate BCF output\n");
                fprintf(stderr, "         -u          do not compress BCF output\n");
                fprintf(stderr, "         -q INT      filter out alignment with MQ smaller than INT [%d]\n", mplp.min_mq);
                fprintf(stderr, "         -g          generate BCF output\n");
                fprintf(stderr, "         -u          do not compress BCF output\n");

+               fprintf(stderr, "         -B          disable BAQ computation\n");

                fprintf(stderr, "\n");
                fprintf(stderr, "Notes: Assuming diploid individuals.\n\n");
                return 1;
                fprintf(stderr, "\n");
                fprintf(stderr, "Notes: Assuming diploid individuals.\n\n");
                return 1;

diff --git a/bam_sort.c b/bam_sort.c
index 90ecddc26c171d112a698cdcba99bb03aebf6d69..76ab793196ca76fc5a63d619e230cf0fb5f59f1e 100644 (file)
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -137,11 +137,15 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch
                                // check that they are consistent with the existing binary list
                                // of reference information.
                                if (hheaders->n_targets > 0) {
                                // check that they are consistent with the existing binary list
                                // of reference information.
                                if (hheaders->n_targets > 0) {

-                                       if (hout->n_targets != hheaders->n_targets)
+                                       if (hout->n_targets != hheaders->n_targets) {

                                                fprintf(stderr, "[bam_merge_core] number of @SQ headers in `%s' differs from number of target sequences", headers);
                                                fprintf(stderr, "[bam_merge_core] number of @SQ headers in `%s' differs from number of target sequences", headers);

+                                               if (!reg) return -1;
+                                       }

                                        for (j = 0; j < hout->n_targets; ++j)
                                        for (j = 0; j < hout->n_targets; ++j)

-                                               if (strcmp(hout->target_name[j], hheaders->target_name[j]) != 0)
+                                               if (strcmp(hout->target_name[j], hheaders->target_name[j]) != 0) {

                                                        fprintf(stderr, "[bam_merge_core] @SQ header '%s' in '%s' differs from target sequence", hheaders->target_name[j], headers);
                                                        fprintf(stderr, "[bam_merge_core] @SQ header '%s' in '%s' differs from target sequence", hheaders->target_name[j], headers);

+                                                       if (!reg) return -1;
+                                               }

                                }
                                swap_header_text(hout, hheaders);
                                bam_header_destroy(hheaders);
                                }
                                swap_header_text(hout, hheaders);
                                bam_header_destroy(hheaders);

diff --git a/bamtk.c b/bamtk.c
index 7bc87567f9b171cbee165b28bf178795e8e95594..aabc5ae76ed46b4ca79bf447fdcee6333668140d 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
 #endif
 
 #ifndef PACKAGE_VERSION

-#define PACKAGE_VERSION "0.1.8-21 (r780)"
+#define PACKAGE_VERSION "0.1.8-22 (r781)"

 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);

diff --git a/samtools.1 b/samtools.1
index 2bfeb432feb4163b189ccf028dd65907c0a99f3b..77b5a22f62b6233f513d5695ad98a61d5474cdff 100644 (file)
--- a/samtools.1
+++ b/samtools.1
@@ -1,4 +1,4 @@
-.TH samtools 1 "2 October 2010" "samtools-0.1.8" "Bioinformatics tools"
+.TH samtools 1 "27 October 2010" "samtools-0.1.9" "Bioinformatics tools"

 .SH NAME
 .PP
 samtools - Utilities for the Sequence Alignment/Map (SAM) format
 .SH NAME
 .PP
 samtools - Utilities for the Sequence Alignment/Map (SAM) format


@@ -18,7 +18,7 @@ samtools merge out.bam in1.bam in2.bam in3.bam
 .PP
 samtools faidx ref.fasta
 .PP
 .PP
 samtools faidx ref.fasta
 .PP

-samtools pileup -f ref.fasta aln.sorted.bam
+samtools pileup -vcf ref.fasta aln.sorted.bam

 .PP
 samtools mpileup -C50 -agf ref.fasta -r chr3:1,000-2,000 in1.bam in2.bam
 .PP
 .PP
 samtools mpileup -C50 -agf ref.fasta -r chr3:1,000-2,000 in1.bam in2.bam
 .PP


@@ -65,10 +65,12 @@ format: `chr2' (the whole chr2), `chr2:1000000' (region starting from
 .B -b
 Output in the BAM format.
 .TP
 .B -b
 Output in the BAM format.
 .TP

-.B -u
-Output uncompressed BAM. This option saves time spent on
-compression/decomprssion and is thus preferred when the output is piped
-to another samtools command.
+.BI -f " INT"
+Only output alignments with all bits in INT present in the FLAG
+field. INT can be in hex in the format of /^0x[0-9A-F]+/ [0]
+.TP
+.BI -F " INT"
+Skip alignments with bits present in INT [0]

 .TP
 .B -h
 Include the header in the output.
 .TP
 .B -h
 Include the header in the output.


@@ -76,12 +78,29 @@ Include the header in the output.
 .B -H
 Output the header only.
 .TP
 .B -H
 Output the header only.
 .TP

+.BI -l " STR"
+Only output reads in library STR [null]
+.TP
+.BI -o " FILE"
+Output file [stdout]
+.TP
+.BI -q " INT"
+Skip alignments with MAPQ smaller than INT [0]
+.TP
+.BI -r " STR"
+Only output reads in read group STR [null]
+.TP
+.BI -R " FILE"
+Output reads in read groups listed in
+.I FILE
+[null]
+.TP

 .B -S
 Input is in SAM. If @SQ header lines are absent, the
 .B `-t'
 option is required.
 .TP
 .B -S
 Input is in SAM. If @SQ header lines are absent, the
 .B `-t'
 option is required.
 .TP

-.B -t FILE
+.BI -t " FILE"

 This file is TAB-delimited. Each line must contain the reference name
 and the length of the reference, one line for each distinct reference;
 additional fields are ignored. This file also defines the order of the
 This file is TAB-delimited. Each line must contain the reference name
 and the length of the reference, one line for each distinct reference;
 additional fields are ignored. This file also defines the order of the


@@ -92,29 +111,10 @@ can be used as this
 .I <in.ref_list>
 file.
 .TP
 .I <in.ref_list>
 file.
 .TP

-.B -o FILE
-Output file [stdout]
-.TP
-.B -f INT
-Only output alignments with all bits in INT present in the FLAG
-field. INT can be in hex in the format of /^0x[0-9A-F]+/ [0]
-.TP
-.B -F INT
-Skip alignments with bits present in INT [0]
-.TP
-.B -q INT
-Skip alignments with MAPQ smaller than INT [0]
-.TP
-.B -l STR
-Only output reads in library STR [null]
-.TP
-.B -r STR
-Only output reads in read group STR [null]
-.TP
-.B -R FILE
-Output reads in read groups listed in
-.I FILE
-[null]
+.B -u
+Output uncompressed BAM. This option saves time spent on
+compression/decomprssion and is thus preferred when the output is piped
+to another samtools command.

 .RE
 
 .TP
 .RE
 
 .TP


@@ -128,8 +128,10 @@ viewing the same reference sequence.
 
 .TP
 .B pileup
 
 .TP
 .B pileup

-samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l in.site_list]
-[-iscgS2] [-T theta] [-N nHap] [-r pairDiffRate] <in.bam>|<in.sam>
+samtools pileup [-2sSBicv] [-f in.ref.fasta] [-t in.ref_list] [-l
+in.site_list] [-C capMapQ] [-M maxMapQ] [-T theta] [-N nHap] [-r
+pairDiffRate] [-m mask] [-d maxIndelDepth] [-G indelPrior]
+<in.bam>|<in.sam>

 
 Print the alignment in the pileup format. In the pileup format, each
 line represents a genomic position, consisting of chromosome name,
 
 Print the alignment in the pileup format. In the pileup format, each
 line represents a genomic position, consisting of chromosome name,


@@ -138,17 +140,17 @@ mapping qualities. Information on match, mismatch, indel, strand,
 mapping quality and start and end of a read are all encoded at the read
 base column. At this column, a dot stands for a match to the reference
 base on the forward strand, a comma for a match on the reverse strand,
 mapping quality and start and end of a read are all encoded at the read
 base column. At this column, a dot stands for a match to the reference
 base on the forward strand, a comma for a match on the reverse strand,

-`ACGTN' for a mismatch on the forward strand and `acgtn' for a mismatch
-on the reverse strand. A pattern `\\+[0-9]+[ACGTNacgtn]+' indicates
-there is an insertion between this reference position and the next
-reference position. The length of the insertion is given by the integer
-in the pattern, followed by the inserted sequence. Similarly, a pattern
-`-[0-9]+[ACGTNacgtn]+' represents a deletion from the reference. The
-deleted bases will be presented as `*' in the following lines. Also at
-the read base column, a symbol `^' marks the start of a read segment
-which is a contiguous subsequence on the read separated by `N/S/H' CIGAR
-operations. The ASCII of the character following `^' minus 33 gives the
-mapping quality. A symbol `$' marks the end of a read segment.
+a '>' or '<' for a reference skip, `ACGTN' for a mismatch on the forward
+strand and `acgtn' for a mismatch on the reverse strand. A pattern
+`\\+[0-9]+[ACGTNacgtn]+' indicates there is an insertion between this
+reference position and the next reference position. The length of the
+insertion is given by the integer in the pattern, followed by the
+inserted sequence. Similarly, a pattern `-[0-9]+[ACGTNacgtn]+'
+represents a deletion from the reference. The deleted bases will be
+presented as `*' in the following lines. Also at the read base column, a
+symbol `^' marks the start of a read. The ASCII of the character
+following `^' minus 33 gives the mapping quality. A symbol `$' marks the
+end of a read segment.

 
 If option
 .B -c
 
 If option
 .B -c


@@ -168,88 +170,94 @@ The position of indels is offset by -1.
 .B OPTIONS:
 .RS
 .TP 10
 .B OPTIONS:
 .RS
 .TP 10

-.B -s
-Print the mapping quality as the last column. This option makes the
-output easier to parse, although this format is not space efficient.
+.B -B
+Disable the BAQ computation. See the
+.B mpileup
+command for details.

 .TP
 .TP

-.B -S
-The input file is in SAM.
+.B -c
+Call the consensus sequence using SOAPsnp consensus model. Options
+.BR -T ", " -N ", " -I " and " -r
+are only effective when
+.BR -c " or " -g
+is in use.

 .TP
 .TP

-.B -i
-Only output pileup lines containing indels.
+.BI -C " INT"
+Coefficient for downgrading the mapping quality of poorly mapped
+reads. See the
+.B mpileup
+command for details. [0]
+.TP
+.BI -d " INT"
+Use the first
+.I NUM
+reads in the pileup for indel calling for speed up. Zero for unlimited. [1024]

 .TP
 .TP

-.B -f FILE
+.BI -f " FILE"

 The reference sequence in the FASTA format. Index file
 .I FILE.fai
 will be created if
 absent.
 .TP
 The reference sequence in the FASTA format. Index file
 .I FILE.fai
 will be created if
 absent.
 .TP

-.B -M INT
-Cap mapping quality at INT [60]
+.B -g
+Generate genotype likelihood in the binary GLFv3 format. This option
+suppresses -c, -i and -s. This option is deprecated by the
+.B mpileup
+command.

 .TP
 .TP

-.B -m INT
+.B -i
+Only output pileup lines containing indels.
+.TP
+.BI -I " INT"
+Phred probability of an indel in sequencing/prep. [40]
+.TP
+.BI -l " FILE"
+List of sites at which pileup is output. This file is space
+delimited. The first two columns are required to be chromosome and
+1-based coordinate. Additional columns are ignored. It is
+recommended to use option
+.TP
+.BI -m " INT"

 Filter reads with flag containing bits in
 Filter reads with flag containing bits in

-.I
-INT
+.I INT

 [1796]
 .TP
 [1796]
 .TP

-.B -d INT
-Use the first
-.I NUM
-reads in the pileup for indel calling for speed up. Zero for unlimited. [0]
+.BI -M " INT"
+Cap mapping quality at INT [60]
+.TP
+.BI -N " INT"
+Number of haplotypes in the sample (>=2) [2]
+.TP
+.BI -r " FLOAT"
+Expected fraction of differences between a pair of haplotypes [0.001]

 .TP
 .TP

-.B -t FILE
+.B -s
+Print the mapping quality as the last column. This option makes the
+output easier to parse, although this format is not space efficient.
+.TP
+.B -S
+The input file is in SAM.
+.TP
+.BI -t " FILE"

 List of reference names ane sequence lengths, in the format described
 for the
 .B import
 command. If this option is present, samtools assumes the input
 .I <in.alignment>
 is in SAM format; otherwise it assumes in BAM format.
 List of reference names ane sequence lengths, in the format described
 for the
 .B import
 command. If this option is present, samtools assumes the input
 .I <in.alignment>
 is in SAM format; otherwise it assumes in BAM format.

-.TP
-.B -l FILE
-List of sites at which pileup is output. This file is space
-delimited. The first two columns are required to be chromosome and
-1-based coordinate. Additional columns are ignored. It is
-recommended to use option

 .B -s
 together with
 .B -l
 as in the default format we may not know the mapping quality.
 .TP
 .B -s
 together with
 .B -l
 as in the default format we may not know the mapping quality.
 .TP

-.B -c
-Call the consensus sequence using SOAPsnp consensus model. Options
-.B -T,
-.B -N,
-.B -I
-and
-.B -r
-are only effective when
-.B -c
-or
-.B -g
-is in use.
-.TP
-.B -g
-Generate genotype likelihood in the binary GLFv3 format. This option
-suppresses -c, -i and -s.
-.TP
-.B -T FLOAT
+.BI -T " FLOAT"

 The theta parameter (error dependency coefficient) in the maq consensus
 calling model [0.85]
 The theta parameter (error dependency coefficient) in the maq consensus
 calling model [0.85]

-.TP
-.B -N INT
-Number of haplotypes in the sample (>=2) [2]
-.TP
-.B -r FLOAT
-Expected fraction of differences between a pair of haplotypes [0.001]
-.TP
-.B -I INT
-Phred probability of an indel in sequencing/prep. [40]

 .RE
 
 .TP
 .B mpileup
 .RE
 
 .TP
 .B mpileup

-samtools mpileup [-aug] [-C coef] [-r reg] [-f in.fa] [-l list] [-M capMapQ] [-Q minBaseQ] [-q minMapQ] in.bam [in2.bam [...]]
+samtools mpileup [-Bug] [-C capQcoef] [-r reg] [-f in.fa] [-l list] [-M capMapQ] [-Q minBaseQ] [-q minMapQ] in.bam [in2.bam [...]]

 
 Generate BCF or pileup for one or multiple BAM files. Alignment records
 are grouped by sample identifiers in @RG header lines. If sample
 
 Generate BCF or pileup for one or multiple BAM files. Alignment records
 are grouped by sample identifiers in @RG header lines. If sample


@@ -258,38 +266,40 @@ identifiers are absent, each input file is regarded as one sample.
 .B OPTIONS:
 .RS
 .TP 8
 .B OPTIONS:
 .RS
 .TP 8

-.B -a
-Perform HMM realignment to compute base alignment quality (BAQ). Base
-quality will be capped by BAQ.
+.B -B
+Disable probabilistic realignment for the computation of base alignment
+quality (BAQ). BAQ is the Phred-scaled probability of a read base being
+misaligned. Applying this option greatly helps to reduce false SNPs
+caused by misalignments.

 .TP
 .TP

-.B -g
-Compute genotype likelihoods and output them in the binary call format (BCF).
-.TP
-.B -u
-Similar to
-.B -g
-except that the output is uncompressed BCF, which is preferred for pipeing.
-.TP
-.B -C INT
+.BI -C " INT"

 Coefficient for downgrading mapping quality for reads containing
 excessive mismatches. Given a read with a phred-scaled probability q of
 being generated from the mapped position, the new mapping quality is
 about sqrt((INT-q)/INT)*INT. A zero value disables this
 functionality; if enabled, the recommended value is 50. [0]
 .TP
 Coefficient for downgrading mapping quality for reads containing
 excessive mismatches. Given a read with a phred-scaled probability q of
 being generated from the mapped position, the new mapping quality is
 about sqrt((INT-q)/INT)*INT. A zero value disables this
 functionality; if enabled, the recommended value is 50. [0]
 .TP

-.B -f FILE
+.BI -f " FILE"

 The reference file [null]
 .TP
 The reference file [null]
 .TP

-.B -l FILE
+.B -g
+Compute genotype likelihoods and output them in the binary call format (BCF).
+.TP
+.B -u
+Similar to
+.B -g
+except that the output is uncompressed BCF, which is preferred for pipeing.
+.TP
+.BI -l " FILE"

 File containing a list of sites where pileup or BCF is outputted [null]
 .TP
 File containing a list of sites where pileup or BCF is outputted [null]
 .TP

-.B -q INT
+.BI -q " INT"

 Minimum mapping quality for an alignment to be used [0]
 .TP
 Minimum mapping quality for an alignment to be used [0]
 .TP

-.B -Q INT
+.BI -Q " INT"

 Minimum base quality for a base to be considered [13]
 .TP
 Minimum base quality for a base to be considered [13]
 .TP

-.B -r STR
+.BI -r " STR"

 Only generate pileup in region
 .I STR
 [all sites]
 Only generate pileup in region
 .I STR
 [all sites]


@@ -332,7 +342,7 @@ Approximately the maximum required memory. [500000000]
 
 .TP
 .B merge
 
 .TP
 .B merge

-samtools merge [-h inh.sam] [-nr] <out.bam> <in1.bam> <in2.bam> [...]
+samtools merge [-nur] [-h inh.sam] [-R reg] <out.bam> <in1.bam> <in2.bam> [...]

 
 Merge multiple sorted alignments.
 The header reference lists of all the input BAM files, and the @SQ headers of
 
 Merge multiple sorted alignments.
 The header reference lists of all the input BAM files, and the @SQ headers of


@@ -349,7 +359,7 @@ and the headers of other files will be ignored.
 .B OPTIONS:
 .RS
 .TP 8
 .B OPTIONS:
 .RS
 .TP 8

-.B -h FILE
+.BI -h " FILE"

 Use the lines of
 .I FILE
 as `@' headers to be copied to
 Use the lines of
 .I FILE
 as `@' headers to be copied to


@@ -360,12 +370,19 @@ replacing any header lines that would otherwise be copied from
 is actually in SAM format, though any alignment records it may contain
 are ignored.)
 .TP
 is actually in SAM format, though any alignment records it may contain
 are ignored.)
 .TP

+.BI -R " STR"
+Merge files in the specified region indicated by
+.I STR
+.TP

 .B -r
 Attach an RG tag to each alignment. The tag value is inferred from file names.
 .TP
 .B -n
 The input alignments are sorted by read names rather than by chromosomal
 coordinates
 .B -r
 Attach an RG tag to each alignment. The tag value is inferred from file names.
 .TP
 .B -n
 The input alignments are sorted by read names rather than by chromosomal
 coordinates

+.TP
+.B -u
+Uncompressed BAM output

 .RE
 
 .TP
 .RE
 
 .TP


@@ -431,7 +448,7 @@ Treat paired-end reads and single-end reads.
 
 .TP
 .B calmd
 
 .TP
 .B calmd

-samtools calmd [-eubS] <aln.bam> <ref.fasta>
+samtools calmd [-eubSr] [-C capQcoef] <aln.bam> <ref.fasta>

 
 Generate the MD tag. If the MD tag is already present, this command will
 give a warning if the MD tag generated is different from the existing
 
 Generate the MD tag. If the MD tag is already present, this command will
 give a warning if the MD tag generated is different from the existing


@@ -452,6 +469,15 @@ Output compressed BAM
 .TP
 .B -S
 The input is SAM with header lines
 .TP
 .B -S
 The input is SAM with header lines

+.TP
+.BI -C " INT"
+Coefficient to cap mapping quality of poorly mapped reads. See the
+.B pileup
+command for details. [0]
+.TP
+.B -r
+Perform probabilistic realignment to compute BAQ, which will be used to
+cap base quality.

 .RE
 
 .SH SAM FORMAT
 .RE
 
 .SH SAM FORMAT


@@ -501,6 +527,122 @@ _
 0x0400 d       the read is either a PCR or an optical duplicate
 .TE
 
 0x0400 d       the read is either a PCR or an optical duplicate
 .TE
 

+.SH EXAMPLES
+.IP o 2
+Import SAM to BAM when
+.B @SQ
+lines are present in the header:
+
+  samtools view -bS aln.sam > aln.bam
+
+If
+.B @SQ
+lines are absent:
+
+  samtools faidx ref.fa
+  samtools view -bt ref.fa.fai aln.sam > aln.bam
+
+where
+.I ref.fa.fai
+is generated automatically by the
+.B faidx
+command.
+
+.IP o 2
+Attach the
+.B RG
+tag while merging sorted alignments:
+
+  perl -e 'print "@RG\\tID:ga\\tSM:hs\\tLB:ga\\tPL:Illumina\\n@RG\\tID:454\\tSM:hs\\tLB:454\\tPL:454\\n"' > rg.txt
+  samtools merge -rh rg.txt merged.bam ga.bam 454.bam
+
+The value in a
+.B RG
+tag is determined by the file name the read is coming from. In this
+example, in the
+.IR merged.bam ,
+reads from
+.I ga.bam
+will be attached 
+.IR RG:Z:ga ,
+while reads from
+.I 454.bam
+will be attached
+.IR RG:Z:454 .
+
+.IP o 2
+Call SNPs and short indels for one diploid individual:
+
+  samtools pileup -vcf ref.fa aln.bam > var.raw.plp
+  samtools.pl varFilter -D 100 var.raw.plp > var.flt.plp
+  awk '($3=="*"&&$6>=50)||($3!="*"&&$6>=20)' var.flt.plp > var.final.plp
+
+The
+.B -D
+option of varFilter controls the maximum read depth, which should be
+adjusted to about twice the average read depth.  One may consider to add
+.B -C50
+to
+.B pileup
+if mapping quality is overestimated for reads containing excessive
+mismatches. Applying this option usually helps
+.B BWA-short
+but may not other mappers. It also potentially increases reference
+biases.
+
+.IP o 2
+Call SNPs (not short indels) for multiple diploid individuals:
+
+  samtools mpileup -augf ref.fa *.bam | bcftools view -bcv - > snp.raw.bcf
+  bcftools view snp.raw.bcf | vcfutils.pl filter4vcf -D 2000 | bgzip > snp.flt.vcf.gz
+
+Individuals are identified from the
+.B SM
+tags in the
+.B @RG
+header lines. Individuals can be pooled in one alignment file; one
+individual can also be separated into multiple files. Similarly, one may
+consider to apply
+.B -C50
+to
+.BR mpileup .
+
+.IP o 2
+Derive the allele frequency spectrum (AFS) on a list of sites from multiple individuals:
+
+  samtools mpileup -gf ref.fa *.bam > all.bcf
+  bcftools view -bl sites.list all.bcf > sites.bcf
+  bcftools view -cGP cond2 sites.bcf > /dev/null 2> sites.1.afs
+  bcftools view -cGP sites.1.afs sites.bcf > /dev/null 2> sites.2.afs
+  bcftools view -cGP sites.2.afs sites.bcf > /dev/null 2> sites.3.afs
+  ......
+
+where
+.I sites.list
+contains the list of sites with each line consisting of the reference
+sequence name and position. The following
+.B bcftools
+commands estimate AFS by EM.
+
+.IP o 2
+Dump BAQ applied alignment for other SNP callers:
+
+  samtools calmd -br aln.bam > aln.baq.bam
+
+It adds and corrects the
+.B NM
+and
+.B MD
+tags at the same time. The
+.B calmd
+command also comes with the
+.B -C
+option, the same as the on in
+.B pileup
+and
+.BR mpileup .
+Apply if it helps.
+

 .SH LIMITATIONS
 .PP
 .IP o 2
 .SH LIMITATIONS
 .PP
 .IP o 2