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* modify the filtering rule: also filter SNPs around filtered indels
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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2010-11-18 Heng Lifixed a bug in printing MNPs
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2010-11-18 Heng Liminor change to how seqQ is applied
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2010-11-18 Heng Li * samtools-0.1.10 (r831)
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2010-11-17 Heng LiRelease samtools-0.1.10 (r829)
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2010-11-17 Heng Liupdate version information: samtools-0.1.9-20 (r828)
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2010-11-16 Heng Libcftools: allow to skip indels
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2010-11-16 Heng Liremove 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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2010-11-13 Heng Li * samtools-0.1.9-13 (r819)
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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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2010-11-11 Heng Li * samtools-0.1.9-10 (r816)
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2010-11-11 Heng Lieffectively 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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2010-11-11 Heng Li * prepare to replace kaln with kprobaln in realignment
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2010-11-10 Heng Lifixed a typo
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2010-11-10 Heng Liuse 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 Liminor 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 Libcftools: compute equal-tail (Bayesian) credible interval
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2010-11-09 Heng Liadded 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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2010-11-08 Heng Lifixed another silly bug in mpileup's indel caller
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2010-11-08 Heng Lifixed a silly bug in the indel caller
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2010-11-08 Heng LiIncorporate 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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2010-11-08 Heng Liindel calling is apparently working, but more information...
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2010-11-08 Heng Lifixed a few bugs in the indel caller. Probably there...
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2010-11-08 Heng Liprepare for the indel caller. It is not ready yet.
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2010-11-05 Heng LiRevert 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 Lifor backup. no effective changes
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2010-11-03 Heng Lifixed a minor problem in the example coming with kprobaln.c
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2010-11-02 Heng LiSeparate 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 LiOptionally output "DP", the individual read depth
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2010-10-28 Heng Liacknowledge Petr and John who have greatly contributed...
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2010-10-28 Heng LiRelease samtools-0.1.9 (r783)
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2010-10-27 Heng Lifixed a silly bug in pileup
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2010-10-27 Heng Li * samtools-0.1.8-22 (r781)
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2010-10-27 Heng Li * samtools-0.1.8-21 (r780)
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2010-10-27 Heng Liimprove 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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2010-10-26 Heng Liremove 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 Liadded another toy example
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2010-10-14 Heng Liimprove the LD statistics
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2010-10-13 Heng Li * a minor fix to the -L option
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2010-10-12 Heng Lia minor change
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2010-10-12 Heng Liforget 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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2010-10-11 Heng Liadded filter for samtools/bcftools genetated VCFs
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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 LiI 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 Limark samtools-0.1.8-16 (r759)
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2010-09-30 Heng Liround to the nearest integer
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2010-09-28 Heng LiI was trying to accelerate ka_prob_glocal() as this...
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2010-09-28 Heng Lithis is interesting. multiplication is much faster...
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2010-09-28 Heng Liminor changes
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2010-09-28 Heng Liprob_realn() seems working!
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2010-09-28 Heng Liminor
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2010-09-28 Heng LiConvert phredQ to probabilities
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2010-09-28 Heng LiImplement the glocal HMM; discard the extention HMM
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2010-09-28 Heng Liimprove numerical stability
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2010-09-28 Heng Limore comments
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2010-09-28 Heng Lifixed a bug in banded DP
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2010-09-28 Heng Li * fixed that weird issue.
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2010-09-28 Heng LiMore comments. This version seems working, but something...
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2010-09-27 Heng LiA little code cleanup. Now the forward and backback...
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2010-09-27 Heng Li...
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2010-09-22 Heng Li * samtools-0.1.8-15 (r379)
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2010-09-20 Heng Li * merge files region-by-region. work on small examples...
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2010-09-20 Heng Liimprove qstats by checking the alleles as well
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2010-09-17 Heng Liconvert UCSC SNP SQL dump to VCF
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2010-09-17 Heng Lihapmap2vcf convertor
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2010-09-17 Heng Li * added comments
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2010-09-17 Heng Li * put n_smpl to "bcf1_t" to simplify API a little
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2010-09-17 Heng Lifixed a bug in indexing
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2010-09-16 Heng Li * fixed a bug in capQ
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2010-09-16 Heng Li * fixed a bug in razip: -c will delete the input file
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2010-09-16 Heng Li * samtools-0.1.8-14 (r727)
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2010-09-16 Heng Li * added varFilter to vcfutils.pl
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2010-09-15 Heng Li * convert BCF to QCALL input
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