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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
2010-08-09	Heng Li	* fixed a bug in kstrtok@kstring.c	commit \| commitdiff \| tree
2010-08-09	Heng Li	* improved kstring (added kstrtok)	commit \| commitdiff \| tree
2010-08-09	Heng Li	help messages	commit \| commitdiff \| tree
2010-08-09	Heng Li	perform single-tail test for ED4	commit \| commitdiff \| tree
2010-08-09	Heng Li	* test depth, end distance and HWE	commit \| commitdiff \| tree
2010-08-08	Heng Li	reimplement incomplete gamma functions. no copy-paste	commit \| commitdiff \| tree
2010-08-07	Heng Li	* bcftools: add HWE (no testing for now)	commit \| commitdiff \| tree
2010-08-06	Heng Li	* Special functions: log(gamma()), erfc(), P(a,x)...	commit \| commitdiff \| tree
2010-08-06	Heng Li	Fisher's exact test	commit \| commitdiff \| tree
2010-08-06	Heng Li	* samtools-0.1.8-11 (r672)	commit \| commitdiff \| tree
2010-08-05	Heng Li	* the code base is stablized again.	commit \| commitdiff \| tree
2010-08-05	Heng Li	minor	commit \| commitdiff \| tree
2010-08-05	Heng Li	unfinished vcf parser	commit \| commitdiff \| tree
2010-08-05	Heng Li	* added prelimiary VCF parser (not finished)	commit \| commitdiff \| tree
2010-08-04	Heng Li	* allow to set min base q	commit \| commitdiff \| tree
2010-08-04	Heng Li	spec	commit \| commitdiff \| tree
2010-08-04	Heng Li	added more examples	commit \| commitdiff \| tree
2010-08-04	Heng Li	fixed compilation error	commit \| commitdiff \| tree
2010-08-04	Heng Li	move bcftools to samtools	commit \| commitdiff \| tree
2010-08-03	Heng Li	fixed another minor bug	commit \| commitdiff \| tree
2010-08-03	Heng Li	* samtools-0.1.8-10 (r658)	commit \| commitdiff \| tree
2010-08-03	Heng Li	* fixed a bug	commit \| commitdiff \| tree
2010-08-02	Heng Li	missing a column in VCF output...	commit \| commitdiff \| tree
2010-08-02	Heng Li	fixed a memory leak	commit \| commitdiff \| tree
2010-08-02	Heng Li	fixed a bug in bcf reader	commit \| commitdiff \| tree
2010-08-02	Heng Li	fixed a bug	commit \| commitdiff \| tree
2010-08-02	Heng Li	* samtools-0.1.8-9 (r649)	commit \| commitdiff \| tree
2010-08-02	Heng Li	Generate binary VCF	commit \| commitdiff \| tree
2010-07-28	Heng Li	* samtools-0.1.8-8 (r644)	commit \| commitdiff \| tree
2010-07-28	Heng Li	* fixed a STUPID bug, which cost me a lot of time.	commit \| commitdiff \| tree
2010-07-28	Heng Li	supposedly this is THE correct implementation, but...	commit \| commitdiff \| tree
2010-07-28	Heng Li	NOT ready yet. Going to make further changes...	commit \| commitdiff \| tree
2010-07-26	Heng Li	* samtools-0.1.8-7 (r639)	commit \| commitdiff \| tree
2010-07-25	Heng Li	* samtools-0.1.8-6 (r638)	commit \| commitdiff \| tree
2010-07-24	Heng Li	minor changes	commit \| commitdiff \| tree
2010-07-24	Heng Li	minor tweaks	commit \| commitdiff \| tree
2010-07-24	Heng Li	posterior expectation FINALLY working. I am so tired...	commit \| commitdiff \| tree
2010-07-23	Heng Li	another minor fix to mpileup	commit \| commitdiff \| tree
2010-07-23	Heng Li	added the format column	commit \| commitdiff \| tree
2010-07-23	Heng Li	added an alternative prior	commit \| commitdiff \| tree
2010-07-23	Heng Li	calculate posterior allele frequency	commit \| commitdiff \| tree
2010-07-23	Heng Li	* samtools-0.1.8-3 (r627)	commit \| commitdiff \| tree
2010-07-22	Heng Li	* preliminary multisample SNP caller.	commit \| commitdiff \| tree
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