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2010-11-08	Heng Li	Incorporate patches by Marcel Martin for read counting.	commit \| commitdiff \| tree
2010-11-08	Heng Li	* samtools-0.1.9-2 (r797)	commit \| commitdiff \| tree
2010-11-08	Heng Li	indel calling is apparently working, but more information...	commit \| commitdiff \| tree
2010-11-08	Heng Li	fixed a few bugs in the indel caller. Probably there...	commit \| commitdiff \| tree
2010-11-08	Heng Li	prepare for the indel caller. It is not ready yet.	commit \| commitdiff \| tree
2010-11-05	Heng Li	Revert to r790. The recent changes are not good...	commit \| commitdiff \| tree
2010-11-05	Heng Li	* this revision is UNSTABLE	commit \| commitdiff \| tree
2010-11-05	Heng Li	for backup. no effective changes	commit \| commitdiff \| tree
2010-11-03	Heng Li	fixed a minor problem in the example coming with kprobaln.c	commit \| commitdiff \| tree
2010-11-02	Heng Li	Separate kaln and kprobaln as I am preparing further...	commit \| commitdiff \| tree
2010-10-30	Heng Li	* samtools-0.1.9-2 (r787)	commit \| commitdiff \| tree
2010-10-29	Heng Li	* samtools-0.1.9-1 (r786)	commit \| commitdiff \| tree
2010-10-29	Heng Li	Optionally output "DP", the individual read depth	commit \| commitdiff \| tree
2010-10-28	Heng Li	acknowledge Petr and John who have greatly contributed...	commit \| commitdiff \| tree
2010-10-28	Heng Li	Release samtools-0.1.9 (r783)	commit \| commitdiff \| tree
2010-10-27	Heng Li	fixed a silly bug in pileup	commit \| commitdiff \| tree
2010-10-27	Heng Li	* samtools-0.1.8-22 (r781)	commit \| commitdiff \| tree
2010-10-27	Heng Li	* samtools-0.1.8-21 (r780)	commit \| commitdiff \| tree
2010-10-27	Heng Li	improve pileup a little bit	commit \| commitdiff \| tree
2010-10-27	Heng Li	* samtools-0.1.8-20 (r778)	commit \| commitdiff \| tree
2010-10-26	Heng Li	* samtools-0.1.8-19 (r777)	commit \| commitdiff \| tree
2010-10-26	Heng Li	remove local realignment (probabilistic realignment...	commit \| commitdiff \| tree
2010-10-19	Heng Li	* Minor code changes. No real effect.	commit \| commitdiff \| tree
2010-10-19	Heng Li	added another toy example	commit \| commitdiff \| tree
2010-10-14	Heng Li	improve the LD statistics	commit \| commitdiff \| tree
2010-10-13	Heng Li	* a minor fix to the -L option	commit \| commitdiff \| tree
2010-10-12	Heng Li	a minor change	commit \| commitdiff \| tree
2010-10-12	Heng Li	forget to add the key file	commit \| commitdiff \| tree
2010-10-12	Heng Li	* vcfutils.pl: fixed a typo in help message	commit \| commitdiff \| tree
2010-10-11	Heng Li	added filter for samtools/bcftools genetated VCFs	commit \| commitdiff \| tree
2010-10-05	Heng Li	* removed a comment line in kaln.c	commit \| commitdiff \| tree
2010-10-03	Heng Li	* samtools-0.1.8-18 (r763)	commit \| commitdiff \| tree
2010-10-03	Heng Li	* vcfutils.pl qstats: calculate marginal ts/tv	commit \| commitdiff \| tree
2010-10-01	Heng Li	I am changing the gap open probability back to 0.001...	commit \| commitdiff \| tree
2010-10-01	Heng Li	* samtools-0.1.8-17 (r760)	commit \| commitdiff \| tree
2010-09-30	Heng Li	mark samtools-0.1.8-16 (r759)	commit \| commitdiff \| tree
2010-09-30	Heng Li	round to the nearest integer	commit \| commitdiff \| tree
2010-09-28	Heng Li	I was trying to accelerate ka_prob_glocal() as this...	commit \| commitdiff \| tree
2010-09-28	Heng Li	this is interesting. multiplication is much faster...	commit \| commitdiff \| tree
2010-09-28	Heng Li	minor changes	commit \| commitdiff \| tree
2010-09-28	Heng Li	prob_realn() seems working!	commit \| commitdiff \| tree
2010-09-28	Heng Li	minor	commit \| commitdiff \| tree
2010-09-28	Heng Li	Convert phredQ to probabilities	commit \| commitdiff \| tree
2010-09-28	Heng Li	Implement the glocal HMM; discard the extention HMM	commit \| commitdiff \| tree
2010-09-28	Heng Li	improve numerical stability	commit \| commitdiff \| tree
2010-09-28	Heng Li	more comments	commit \| commitdiff \| tree
2010-09-28	Heng Li	fixed a bug in banded DP	commit \| commitdiff \| tree
2010-09-28	Heng Li	* fixed that weird issue.	commit \| commitdiff \| tree
2010-09-28	Heng Li	More comments. This version seems working, but something...	commit \| commitdiff \| tree
2010-09-27	Heng Li	A little code cleanup. Now the forward and backback...	commit \| commitdiff \| tree
2010-09-27	Heng Li	...	commit \| commitdiff \| tree
2010-09-22	Heng Li	* samtools-0.1.8-15 (r379)	commit \| commitdiff \| tree
2010-09-20	Heng Li	* merge files region-by-region. work on small examples...	commit \| commitdiff \| tree
2010-09-20	Heng Li	improve qstats by checking the alleles as well	commit \| commitdiff \| tree
2010-09-17	Heng Li	convert UCSC SNP SQL dump to VCF	commit \| commitdiff \| tree
2010-09-17	Heng Li	hapmap2vcf convertor	commit \| commitdiff \| tree
2010-09-17	Heng Li	* added comments	commit \| commitdiff \| tree
2010-09-17	Heng Li	* put n_smpl to "bcf1_t" to simplify API a little	commit \| commitdiff \| tree
2010-09-17	Heng Li	fixed a bug in indexing	commit \| commitdiff \| tree
2010-09-16	Heng Li	* fixed a bug in capQ	commit \| commitdiff \| tree
2010-09-16	Heng Li	* fixed a bug in razip: -c will delete the input file	commit \| commitdiff \| tree
2010-09-16	Heng Li	* samtools-0.1.8-14 (r727)	commit \| commitdiff \| tree
2010-09-16	Heng Li	* added varFilter to vcfutils.pl	commit \| commitdiff \| tree
2010-09-15	Heng Li	* convert BCF to QCALL input	commit \| commitdiff \| tree
2010-09-15	Heng Li	dynamic band width in realignment	commit \| commitdiff \| tree
2010-09-15	Heng Li	fixed a bug in realignment	commit \| commitdiff \| tree
2010-09-15	Heng Li	fixed a minor issue	commit \| commitdiff \| tree
2010-09-14	Heng Li	fixed a bug in realignment	commit \| commitdiff \| tree
2010-09-14	Heng Li	minor changes. It is BUGGY now!	commit \| commitdiff \| tree
2010-09-14	Heng Li	* aggressive gapped aligner is implemented in calmd.	commit \| commitdiff \| tree
2010-09-08	Heng Li	* samtools-0.1.8-13 (r715)	commit \| commitdiff \| tree
2010-09-03	Heng Li	quite a lot changes to the contrast caller, but I still...	commit \| commitdiff \| tree
2010-09-03	Heng Li	* changed 3.434 to 4.343 (typo!)	commit \| commitdiff \| tree
2010-09-02	Heng Li	SNP calling from the GL field	commit \| commitdiff \| tree
2010-09-01	Heng Li	fixed another problem	commit \| commitdiff \| tree
2010-09-01	Heng Li	* fixed bugs in parsing VCF	commit \| commitdiff \| tree
2010-09-01	Heng Li	Do not compile _BCF_QUAD by default	commit \| commitdiff \| tree
2010-09-01	Heng Li	Write the correct ALT and PL in the SNP calling mode.	commit \| commitdiff \| tree
2010-09-01	Heng Li	more commands for my own uses	commit \| commitdiff \| tree
2010-09-01	Heng Li	Utilities for processing VCF	commit \| commitdiff \| tree
2010-08-31	Heng Li	preliminary contrast variant caller	commit \| commitdiff \| tree
2010-08-31	Heng Li	z' and z'' can be calculated	commit \| commitdiff \| tree
2010-08-31	Heng Li	* rename vcfout.c as call1.c	commit \| commitdiff \| tree
2010-08-24	Heng Li	fixed a bug in calculating the t statistics	commit \| commitdiff \| tree
2010-08-24	Heng Li	* samtools-0.1.8-13 (r698)	commit \| commitdiff \| tree
2010-08-24	Heng Li	added regularized incomplete beta function	commit \| commitdiff \| tree
2010-08-23	Heng Li	change the default correlation coefficient	commit \| commitdiff \| tree
2010-08-23	Heng Li	print QUAL as floating numbers	commit \| commitdiff \| tree
2010-08-23	Heng Li	* samtools-0.1.8-12 (r692)	commit \| commitdiff \| tree
2010-08-23	Heng Li	remove VCF output in mpileup	commit \| commitdiff \| tree
2010-08-23	Heng Li	* use the revised MAQ error model for mpileup	commit \| commitdiff \| tree
2010-08-20	Heng Li	added revised MAQ error model	commit \| commitdiff \| tree
2010-08-18	Heng Li	allow to read the prior from the error output. EM iteration...	commit \| commitdiff \| tree
2010-08-17	Heng Li	* write a little more VCF header	commit \| commitdiff \| tree
2010-08-17	Heng Li	use float for QUAL	commit \| commitdiff \| tree
2010-08-14	Heng Li	faster for large sample size (in principle)	commit \| commitdiff \| tree
2010-08-14	Heng Li	* a numerically stable method to calculate z_{jk}	commit \| commitdiff \| tree
2010-08-12	Heng Li	fixed an issue in parsing integer	commit \| commitdiff \| tree
2010-08-09	Heng Li	do not print refname if file is converted from VCF	commit \| commitdiff \| tree
2010-08-09	Heng Li	* parse PL	commit \| commitdiff \| tree
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