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* vcfutils.pl qstats: calculate marginal ts/tv
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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2010-08-09 Heng Lihelp messages
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2010-08-09 Heng Liperform single-tail test for ED4
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2010-08-09 Heng Li * test depth, end distance and HWE
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2010-08-08 Heng Lireimplement incomplete gamma functions. no copy-paste
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2010-08-07 Heng Li * bcftools: add HWE (no testing for now)
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2010-08-06 Heng Li * Special functions: log(gamma()), erfc(), P(a,x)...
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2010-08-06 Heng LiFisher's exact test
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2010-08-06 Heng Li * samtools-0.1.8-11 (r672)
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2010-08-05 Heng Li * the code base is stablized again.
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2010-08-05 Heng Liminor
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2010-08-05 Heng Liunfinished vcf parser
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2010-08-05 Heng Li * added prelimiary VCF parser (not finished)
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2010-08-04 Heng Li * allow to set min base q
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2010-08-04 Heng Lispec
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2010-08-04 Heng Liadded more examples
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2010-08-04 Heng Lifixed compilation error
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2010-08-04 Heng Limove bcftools to samtools
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2010-08-03 Heng Lifixed another minor bug
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2010-08-03 Heng Li * samtools-0.1.8-10 (r658)
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2010-08-03 Heng Li * fixed a bug
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2010-08-02 Heng Limissing a column in VCF output...
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2010-08-02 Heng Lifixed a memory leak
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2010-08-02 Heng Lifixed a bug in bcf reader
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2010-08-02 Heng Lifixed a bug
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2010-08-02 Heng Li * samtools-0.1.8-9 (r649)
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2010-08-02 Heng LiGenerate binary VCF
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2010-07-28 Heng Li * samtools-0.1.8-8 (r644)
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2010-07-28 Heng Li * fixed a STUPID bug, which cost me a lot of time.
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2010-07-28 Heng Lisupposedly this is THE correct implementation, but...
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2010-07-28 Heng LiNOT ready yet. Going to make further changes...
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