| 2010-12-02 |
Heng Li | a possible fix to DP4=0,0,0,0; have not tested, but...
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| 2010-12-02 |
Heng Li | Release samtools-0.1.12
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| 2010-12-02 |
Heng Li | * samtools-0.1.11-1 (r858)
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| 2010-12-01 |
Heng Li | fixed a memory leak in bam_fetch()
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| 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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| 2010-11-20 |
Heng Li | * samtools-0.1.10-9 (r844)
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| 2010-11-20 |
Heng Li | In merging, if -R is specified, do not abort if the...
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| 2010-11-19 |
Heng Li | * samtools-0.1.10 (r841)
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| 2010-11-19 |
Heng Li | * samtools-0.1.10-4 (r840)
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| 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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| 2010-11-18 |
Heng Li | * samtools-r836
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| 2010-11-18 |
Heng Li | * modify the filtering rule: also filter SNPs around...
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| 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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| 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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| 2010-11-17 |
Heng Li | update version information: samtools-0.1.9-20 (r828)
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| 2010-11-16 |
Heng Li | bcftools: allow to skip indels
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| 2010-11-16 |
Heng Li | remove ZQ if both BQ and ZQ are present
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| 2010-11-16 |
Heng Li | * samtools-0.1.9-18 (r825)
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| 2010-11-16 |
Heng Li | * samtools-0.1.9-17 (r824)
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| 2010-11-15 |
Heng Li | * samtools-0.1.9-r823
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| 2010-11-15 |
Heng Li | * samtools-0.1.9-16 (r822)
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| 2010-11-13 |
Heng Li | * samtools-0.1.9-15 (r821)
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| 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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| 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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| 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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| 2010-11-10 |
Heng Li | use zlib for direct reading when BCF_LITE is in use
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| 2010-11-10 |
Heng Li | * do not use reads containing too many mismatches...
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| 2010-11-10 |
Heng Li | * samtools-0.1.9-8 (r809)
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| 2010-11-10 |
Heng Li | minor change to makefile
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| 2010-11-10 |
Heng Li | * samtools-0.1.9-8 (r807)
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| 2010-11-10 |
Heng Li | bcftools: compute equal-tail (Bayesian) credible interval
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commit | commitdiff | tree |
| 2010-11-09 |
Heng Li | added a double-hit filter to avoid overestimated indel...
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| 2010-11-09 |
Heng Li | * samtools-0.1.9-7 (r804)
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| 2010-11-09 |
Heng Li | * samtools-0.1.9-6 (r803)
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| 2010-11-09 |
Heng Li | * samtools-0.1.9-5 (r802)
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| 2010-11-09 |
Heng Li | * samtools-0.1.9-4 (r801)
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commit | commitdiff | tree |
| 2010-11-08 |
Heng Li | fixed another silly bug in mpileup's indel caller
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commit | commitdiff | tree |
| 2010-11-08 |
Heng Li | fixed a silly bug in the indel caller
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| 2010-11-08 |
Heng Li | Incorporate patches by Marcel Martin for read counting.
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| 2010-11-08 |
Heng Li | * samtools-0.1.9-2 (r797)
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commit | commitdiff | tree |
| 2010-11-08 |
Heng Li | indel calling is apparently working, but more information...
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commit | commitdiff | tree |
| 2010-11-08 |
Heng Li | fixed a few bugs in the indel caller. Probably there...
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commit | commitdiff | tree |
| 2010-11-08 |
Heng Li | prepare for the indel caller. It is not ready yet.
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| 2010-11-05 |
Heng Li | Revert to r790. The recent changes are not good...
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| 2010-11-05 |
Heng Li | * this revision is UNSTABLE
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| 2010-11-05 |
Heng Li | for backup. no effective changes
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| 2010-11-03 |
Heng Li | fixed a minor problem in the example coming with kprobaln.c
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commit | commitdiff | tree |
| 2010-11-02 |
Heng Li | Separate kaln and kprobaln as I am preparing further...
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| 2010-10-30 |
Heng Li | * samtools-0.1.9-2 (r787)
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| 2010-10-29 |
Heng Li | * samtools-0.1.9-1 (r786)
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| 2010-10-29 |
Heng Li | Optionally output "DP", the individual read depth
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| 2010-10-28 |
Heng Li | acknowledge Petr and John who have greatly contributed...
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| 2010-10-28 |
Heng Li | Release samtools-0.1.9 (r783)
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| 2010-10-27 |
Heng Li | fixed a silly bug in pileup
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commit | commitdiff | tree |
| 2010-10-27 |
Heng Li | * samtools-0.1.8-22 (r781)
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commit | commitdiff | tree |
| 2010-10-27 |
Heng Li | * samtools-0.1.8-21 (r780)
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commit | commitdiff | tree |
| 2010-10-27 |
Heng Li | improve pileup a little bit
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| 2010-10-27 |
Heng Li | * samtools-0.1.8-20 (r778)
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| 2010-10-26 |
Heng Li | * samtools-0.1.8-19 (r777)
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commit | commitdiff | tree |
| 2010-10-26 |
Heng Li | remove local realignment (probabilistic realignment...
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| 2010-10-19 |
Heng Li | * Minor code changes. No real effect.
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| 2010-10-19 |
Heng Li | added another toy example
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| 2010-10-14 |
Heng Li | improve the LD statistics
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commit | commitdiff | tree |
| 2010-10-13 |
Heng Li | * a minor fix to the -L option
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commit | commitdiff | tree |
| 2010-10-12 |
Heng Li | a minor change
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commit | commitdiff | tree |
| 2010-10-12 |
Heng Li | forget to add the key file
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| 2010-10-12 |
Heng Li | * vcfutils.pl: fixed a typo in help message
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commit | commitdiff | tree |
| 2010-10-11 |
Heng Li | added filter for samtools/bcftools genetated VCFs
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commit | commitdiff | tree |
| 2010-10-05 |
Heng Li | * removed a comment line in kaln.c
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| 2010-10-03 |
Heng Li | * samtools-0.1.8-18 (r763)
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| 2010-10-03 |
Heng Li | * vcfutils.pl qstats: calculate marginal ts/tv
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| 2010-10-01 |
Heng Li | I am changing the gap open probability back to 0.001...
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| 2010-10-01 |
Heng Li | * samtools-0.1.8-17 (r760)
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| 2010-09-30 |
Heng Li | mark samtools-0.1.8-16 (r759)
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| 2010-09-30 |
Heng Li | round to the nearest integer
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| 2010-09-28 |
Heng Li | I was trying to accelerate ka_prob_glocal() as this...
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| 2010-09-28 |
Heng Li | this is interesting. multiplication is much faster...
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| 2010-09-28 |
Heng Li | minor changes
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commit | commitdiff | tree |
| 2010-09-28 |
Heng Li | prob_realn() seems working!
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| 2010-09-28 |
Heng Li | minor
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commit | commitdiff | tree |
| 2010-09-28 |
Heng Li | Convert phredQ to probabilities
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commit | commitdiff | tree |
| 2010-09-28 |
Heng Li | Implement the glocal HMM; discard the extention HMM
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| 2010-09-28 |
Heng Li | improve numerical stability
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| 2010-09-28 |
Heng Li | more comments
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commit | commitdiff | tree |
| 2010-09-28 |
Heng Li | fixed a bug in banded DP
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commit | commitdiff | tree |
| 2010-09-28 |
Heng Li | * fixed that weird issue.
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commit | commitdiff | tree |
| 2010-09-28 |
Heng Li | More comments. This version seems working, but something...
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