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indel calling is apparently working, but more information needs to be collected
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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2010-09-15 Heng Lidynamic band width in realignment
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2010-09-15 Heng Lifixed a bug in realignment
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2010-09-15 Heng Lifixed a minor issue
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2010-09-14 Heng Lifixed a bug in realignment
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2010-09-14 Heng Liminor changes. It is BUGGY now!
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2010-09-14 Heng Li * aggressive gapped aligner is implemented in calmd.
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2010-09-08 Heng Li * samtools-0.1.8-13 (r715)
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2010-09-03 Heng Liquite a lot changes to the contrast caller, but I still...
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2010-09-03 Heng Li * changed 3.434 to 4.343 (typo!)
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2010-09-02 Heng LiSNP calling from the GL field
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2010-09-01 Heng Lifixed another problem
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2010-09-01 Heng Li * fixed bugs in parsing VCF
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2010-09-01 Heng LiDo not compile _BCF_QUAD by default
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2010-09-01 Heng LiWrite the correct ALT and PL in the SNP calling mode.
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2010-09-01 Heng Limore commands for my own uses
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2010-09-01 Heng LiUtilities for processing VCF
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2010-08-31 Heng Lipreliminary contrast variant caller
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2010-08-31 Heng Liz' and z'' can be calculated
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2010-08-31 Heng Li * rename vcfout.c as call1.c
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2010-08-24 Heng Lifixed a bug in calculating the t statistics
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2010-08-24 Heng Li * samtools-0.1.8-13 (r698)
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2010-08-24 Heng Liadded regularized incomplete beta function
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2010-08-23 Heng Lichange the default correlation coefficient
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2010-08-23 Heng Liprint QUAL as floating numbers
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2010-08-23 Heng Li * samtools-0.1.8-12 (r692)
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2010-08-23 Heng Liremove VCF output in mpileup
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2010-08-23 Heng Li * use the revised MAQ error model for mpileup
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2010-08-20 Heng Liadded revised MAQ error model
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2010-08-18 Heng Liallow to read the prior from the error output. EM iteration...
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2010-08-17 Heng Li * write a little more VCF header
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2010-08-17 Heng Liuse float for QUAL
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2010-08-14 Heng Lifaster for large sample size (in principle)
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2010-08-14 Heng Li * a numerically stable method to calculate z_{jk}
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2010-08-12 Heng Lifixed an issue in parsing integer
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2010-08-09 Heng Lido not print refname if file is converted from VCF
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2010-08-09 Heng Li * parse PL
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2010-08-09 Heng Li * fixed a bug in kstrtok@kstring.c
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2010-08-09 Heng Li * improved kstring (added kstrtok)
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