| 2011-04-17 |
Heng Li | * fixed a bug in bedidx: input BED not sorted
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commit | commitdiff | tree |
| 2011-04-15 |
Heng Li | * Added Brent's method for frequency estimate
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commit | commitdiff | tree |
| 2011-04-10 |
Heng Li | Release samtools-0.1.15 (r949:203)
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commit | commitdiff | tree |
| 2011-04-08 |
Heng Li | * added bam_verbose global variable
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commit | commitdiff | tree |
| 2011-04-01 |
Heng Li | added quality filtering
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commit | commitdiff | tree |
| 2011-04-01 |
Heng Li | fixed a few typos in comments
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commit | commitdiff | tree |
| 2011-04-01 |
Heng Li | Added an example of using mpileup
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commit | commitdiff | tree |
| 2011-03-31 |
Heng Li | * synchronize bgzf in tabix and in samtools
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commit | commitdiff | tree |
| 2011-03-30 |
Heng Li | * added BED support to samtools view and mpileup and...
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commit | commitdiff | tree |
| 2011-03-22 |
Heng Li | Release samtools-0.1.14 (r933:170)
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commit | commitdiff | tree |
| 2011-03-18 |
Heng Li | forget to add this file
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commit | commitdiff | tree |
| 2011-03-18 |
Heng Li | * allow to change the compression level in BAM output
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commit | commitdiff | tree |
| 2011-03-18 |
Heng Li | export2sam.pl-2.3.1, provided by Chris Saunders from...
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commit | commitdiff | tree |
| 2011-03-08 |
Heng Li | added the haploid mode
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commit | commitdiff | tree |
| 2011-03-01 |
Heng Li | Release samtools-0.1.13 (r926:134)
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commit | commitdiff | tree |
| 2011-03-01 |
Heng Li | * optionally drop phase ambiguous reads
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commit | commitdiff | tree |
| 2011-02-28 |
Heng Li | minor changes to a heuristic rule
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commit | commitdiff | tree |
| 2011-02-28 |
Heng Li | * 0.1.12-r924:126
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commit | commitdiff | tree |
| 2011-02-28 |
Heng Li | * put version number in bam.h
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commit | commitdiff | tree |
| 2011-02-25 |
Heng Li | * change the order of PL/GL according to the latest...
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commit | commitdiff | tree |
| 2011-02-25 |
Heng Li | update the BCF spec
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commit | commitdiff | tree |
| 2011-02-25 |
Heng Li | added the phase command
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commit | commitdiff | tree |
| 2011-02-24 |
Heng Li | added "const" to bcf_p1_cal()
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commit | commitdiff | tree |
| 2011-02-24 |
Heng Li | more meaningful BAM truncation message
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commit | commitdiff | tree |
| 2011-02-24 |
Heng Li | * automatically fix errors in GL
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commit | commitdiff | tree |
| 2011-02-11 |
Heng Li | finished VCF->BCF conversion
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commit | commitdiff | tree |
| 2011-02-02 |
Heng Li | fixed a typo in the VCF header
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commit | commitdiff | tree |
| 2011-02-02 |
Heng Li | * fixed an out-of-boundary bug
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commit | commitdiff | tree |
| 2011-01-30 |
Heng Li | * avoid a segfault when network connect fails
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commit | commitdiff | tree |
| 2011-01-27 |
Heng Li | * fixed a rare memory issue in bam_md.c
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commit | commitdiff | tree |
| 2011-01-24 |
Heng Li | fixed two minor bugs in Fisher's exact test
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commit | commitdiff | tree |
| 2011-01-15 |
Heng Li | move bam_nt16_nt4_table[] from bam_maqcns.c to bam_md.c
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commit | commitdiff | tree |
| 2011-01-06 |
Heng Li | * samtools-0.1.12-10 (r896)
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commit | commitdiff | tree |
| 2011-01-04 |
Heng Li | sorry. It is SP not ST
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commit | commitdiff | tree |
| 2011-01-04 |
Heng Li | added ST
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commit | commitdiff | tree |
| 2010-12-21 |
Heng Li | * samtools-0.1.12-9 (r891)
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commit | commitdiff | tree |
| 2010-12-15 |
Heng Li | * samtools-0.1.12-12 (r889)
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commit | commitdiff | tree |
| 2010-12-15 |
Heng Li | When -B is applied to mpileup, still use paired reads...
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commit | commitdiff | tree |
| 2010-12-15 |
Heng Li | * samtools-0.1.12-6 (r887)
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commit | commitdiff | tree |
| 2010-12-14 |
Heng Li | (Arguably) improved the indel caller a tiny bit for...
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commit | commitdiff | tree |
| 2010-12-13 |
Heng Li | * samtools-0.1.12-4 (r884)
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commit | commitdiff | tree |
| 2010-12-12 |
Heng Li | compute max SP and max GQ from sample genotypes
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commit | commitdiff | tree |
| 2010-12-10 |
Heng Li | drop bcf-fix.pl as it is redundant by the latest changes
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commit | commitdiff | tree |
| 2010-12-10 |
Heng Li | * fixed a minor issue in printing VCFs
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commit | commitdiff | tree |
| 2010-12-10 |
Heng Li | Make sure that the GT genotype field is the first
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commit | commitdiff | tree |
| 2010-12-08 |
Heng Li | * samtools-0.1.12-2 (r877)
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commit | commitdiff | tree |
| 2010-12-08 |
Heng Li | a spelling error..
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commit | commitdiff | tree |
| 2010-12-08 |
Heng Li | * samtools-0.1.12-1 (r873)
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commit | commitdiff | tree |
| 2010-12-07 |
Heng Li | fixed a bug in vcf2fq
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commit | commitdiff | tree |
| 2010-12-05 |
Heng Li | added a warning for the Windows version
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commit | commitdiff | tree |
| 2010-12-05 |
Heng Li | In ksprintf(), change "%lf" and "%lg" to "%f" and ...
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commit | commitdiff | tree |
| 2010-12-05 |
Heng Li | bring back the windows support
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commit | commitdiff | tree |
| 2010-12-05 |
Heng Li | Fixed a compiling error when knetfile is not used.
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commit | commitdiff | tree |
| 2010-12-04 |
Heng Li | vcf->fastq
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commit | commitdiff | tree |
| 2010-12-03 |
Heng Li | * remove "-f". Instead always compute consensus quality
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commit | commitdiff | tree |
| 2010-12-03 |
Heng Li | more informative error message
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commit | commitdiff | tree |
| 2010-12-02 |
Heng Li | Release samtools-0.1.12a
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commit | commitdiff | tree |
| 2010-12-02 |
Heng Li | a possible fix to DP4=0,0,0,0; have not tested, but...
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commit | commitdiff | tree |
| 2010-12-02 |
Heng Li | Release samtools-0.1.12
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commit | commitdiff | tree |
| 2010-12-02 |
Heng Li | * samtools-0.1.11-1 (r858)
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commit | commitdiff | tree |
| 2010-12-01 |
Heng Li | fixed a memory leak in bam_fetch()
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commit | commitdiff | tree |
| 2010-11-26 |
Heng Li | * fixed a memory violation
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commit | commitdiff | tree |
| 2010-11-23 |
Heng Li | fixed a typo/bug in r^2 computation
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commit | commitdiff | tree |
| 2010-11-22 |
Heng Li | forget to change the version information
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commit | commitdiff | tree |
| 2010-11-22 |
Heng Li | Release samtools-0.1.11
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commit | commitdiff | tree |
| 2010-11-20 |
Heng Li | * samtools-0.1.10-9 (r844)
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commit | commitdiff | tree |
| 2010-11-20 |
Heng Li | In merging, if -R is specified, do not abort if the...
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commit | commitdiff | tree |
| 2010-11-19 |
Heng Li | * samtools-0.1.10 (r841)
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commit | commitdiff | tree |
| 2010-11-19 |
Heng Li | * samtools-0.1.10-4 (r840)
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commit | commitdiff | tree |
| 2010-11-18 |
Heng Li | * samtools-0.1.10-6 (r839)
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commit | commitdiff | tree |
| 2010-11-18 |
Heng Li | Apply a patch by Rob Davis, which improves fault detection.
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commit | commitdiff | tree |
| 2010-11-18 |
Heng Li | * samtools-r836
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commit | commitdiff | tree |
| 2010-11-18 |
Heng Li | * modify the filtering rule: also filter SNPs around...
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commit | commitdiff | tree |
| 2010-11-18 |
Heng Li | * samtools-0.1.10-4 (r834)
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commit | commitdiff | tree |
| 2010-11-18 |
Heng Li | fixed a bug in printing MNPs
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commit | commitdiff | tree |
| 2010-11-18 |
Heng Li | minor change to how seqQ is applied
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commit | commitdiff | tree |
| 2010-11-18 |
Heng Li | * samtools-0.1.10 (r831)
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commit | commitdiff | tree |
| 2010-11-17 |
Heng Li | Release samtools-0.1.10 (r829)
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commit | commitdiff | tree |
| 2010-11-17 |
Heng Li | update version information: samtools-0.1.9-20 (r828)
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commit | commitdiff | tree |
| 2010-11-16 |
Heng Li | bcftools: allow to skip indels
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commit | commitdiff | tree |
| 2010-11-16 |
Heng Li | remove ZQ if both BQ and ZQ are present
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commit | commitdiff | tree |
| 2010-11-16 |
Heng Li | * samtools-0.1.9-18 (r825)
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commit | commitdiff | tree |
| 2010-11-16 |
Heng Li | * samtools-0.1.9-17 (r824)
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commit | commitdiff | tree |
| 2010-11-15 |
Heng Li | * samtools-0.1.9-r823
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commit | commitdiff | tree |
| 2010-11-15 |
Heng Li | * samtools-0.1.9-16 (r822)
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commit | commitdiff | tree |
| 2010-11-13 |
Heng Li | * samtools-0.1.9-15 (r821)
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commit | commitdiff | tree |
| 2010-11-13 |
Heng Li | * samtools-0.1.9-14 (r820)
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commit | commitdiff | tree |
| 2010-11-13 |
Heng Li | * samtools-0.1.9-13 (r819)
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commit | commitdiff | tree |
| 2010-11-12 |
Heng Li | * samtools-r818
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commit | commitdiff | tree |
| 2010-11-12 |
Heng Li | * samtools-0.1.19-11 (r817)
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commit | commitdiff | tree |
| 2010-11-11 |
Heng Li | * samtools-0.1.9-10 (r816)
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commit | commitdiff | tree |
| 2010-11-11 |
Heng Li | effectively revert to the viterbi version. The forward...
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commit | commitdiff | tree |
| 2010-11-11 |
Heng Li | * samtools-0.1.9-9 (r810)
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commit | commitdiff | tree |
| 2010-11-11 |
Heng Li | * prepare to replace kaln with kprobaln in realignment
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commit | commitdiff | tree |
| 2010-11-10 |
Heng Li | fixed a typo
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commit | commitdiff | tree |
| 2010-11-10 |
Heng Li | use zlib for direct reading when BCF_LITE is in use
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commit | commitdiff | tree |
| 2010-11-10 |
Heng Li | * do not use reads containing too many mismatches...
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commit | commitdiff | tree |
| 2010-11-10 |
Heng Li | * samtools-0.1.9-8 (r809)
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commit | commitdiff | tree |
| 2010-11-10 |
Heng Li | minor change to makefile
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commit | commitdiff | tree |
| 2010-11-10 |
Heng Li | * samtools-0.1.9-8 (r807)
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