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samtools.git
2010-10-27 Heng Li * samtools-0.1.8-22 (r781) commit | commitdiff | tree | snapshot
2010-10-27 Heng Li * samtools-0.1.8-21 (r780) commit | commitdiff | tree | snapshot
2010-10-27 Heng Liimprove pileup a little bit commit | commitdiff | tree | snapshot
2010-10-27 Heng Li * samtools-0.1.8-20 (r778) commit | commitdiff | tree | snapshot
2010-10-26 Heng Li * samtools-0.1.8-19 (r777) commit | commitdiff | tree | snapshot
2010-10-26 Heng Liremove local realignment (probabilistic realignment... commit | commitdiff | tree | snapshot
2010-10-21 On behalf of... Add the relevant filename or region to error messages... commit | commitdiff | tree | snapshot
2010-10-19 Heng Li * Minor code changes. No real effect. commit | commitdiff | tree | snapshot
2010-10-19 Heng Liadded another toy example commit | commitdiff | tree | snapshot
2010-10-14 Heng Liimprove the LD statistics commit | commitdiff | tree | snapshot
2010-10-13 Heng Li * a minor fix to the -L option commit | commitdiff | tree | snapshot
2010-10-12 Heng Lia minor change commit | commitdiff | tree | snapshot
2010-10-12 Heng Liforget to add the key file commit | commitdiff | tree | snapshot
2010-10-12 Heng Li * vcfutils.pl: fixed a typo in help message commit | commitdiff | tree | snapshot
2010-10-11 Heng Liadded filter for samtools/bcftools genetated VCFs commit | commitdiff | tree | snapshot
2010-10-05 Heng Li * removed a comment line in kaln.c commit | commitdiff | tree | snapshot
2010-10-05 Petr DanecekConvert VCF output of "bcftools view -bgcv" to a valid... commit | commitdiff | tree | snapshot
2010-10-03 Heng Li * samtools-0.1.8-18 (r763) commit | commitdiff | tree | snapshot
2010-10-03 Heng Li * vcfutils.pl qstats: calculate marginal ts/tv commit | commitdiff | tree | snapshot
2010-10-01 Heng LiI am changing the gap open probability back to 0.001... commit | commitdiff | tree | snapshot
2010-10-01 Heng Li * samtools-0.1.8-17 (r760) commit | commitdiff | tree | snapshot
2010-09-30 Heng Limark samtools-0.1.8-16 (r759) commit | commitdiff | tree | snapshot
2010-09-30 Heng Liround to the nearest integer commit | commitdiff | tree | snapshot
2010-09-28 Heng LiI was trying to accelerate ka_prob_glocal() as this... commit | commitdiff | tree | snapshot
2010-09-28 Heng Lithis is interesting. multiplication is much faster... commit | commitdiff | tree | snapshot
2010-09-28 Heng Liminor changes commit | commitdiff | tree | snapshot
2010-09-28 Heng Liprob_realn() seems working! commit | commitdiff | tree | snapshot
2010-09-28 Heng Liminor commit | commitdiff | tree | snapshot
2010-09-28 Heng LiConvert phredQ to probabilities commit | commitdiff | tree | snapshot
2010-09-28 Heng LiImplement the glocal HMM; discard the extention HMM commit | commitdiff | tree | snapshot
2010-09-28 Heng Liimprove numerical stability commit | commitdiff | tree | snapshot
2010-09-28 Heng Limore comments commit | commitdiff | tree | snapshot
2010-09-28 Heng Lifixed a bug in banded DP commit | commitdiff | tree | snapshot
2010-09-28 Heng Li * fixed that weird issue. commit | commitdiff | tree | snapshot
2010-09-28 Heng LiMore comments. This version seems working, but somethin... commit | commitdiff | tree | snapshot
2010-09-27 Heng LiA little code cleanup. Now the forward and backback... commit | commitdiff | tree | snapshot
2010-09-27 Heng Li... commit | commitdiff | tree | snapshot
2010-09-27 On behalf of... Abort if merge -h's INH.SAM cannot be opened, just... commit | commitdiff | tree | snapshot
2010-09-24 On behalf of... Use bam_validate1() to detect garbage records in the... commit | commitdiff | tree | snapshot
2010-09-24 On behalf of... Add bam_validate1(). commit | commitdiff | tree | snapshot
2010-09-22 Heng Li * samtools-0.1.8-15 (r379) commit | commitdiff | tree | snapshot
2010-09-22 On behalf of... When bam_read1() returns an error (return value <=... commit | commitdiff | tree | snapshot
2010-09-22 On behalf of... 0 is a successful return value from bam_read1(). ... commit | commitdiff | tree | snapshot
2010-09-20 Heng Li * merge files region-by-region. work on small examples... commit | commitdiff | tree | snapshot
2010-09-20 Heng Liimprove qstats by checking the alleles as well commit | commitdiff | tree | snapshot
2010-09-17 Heng Liconvert UCSC SNP SQL dump to VCF commit | commitdiff | tree | snapshot
2010-09-17 Heng Lihapmap2vcf convertor commit | commitdiff | tree | snapshot
2010-09-17 Heng Li * added comments commit | commitdiff | tree | snapshot
2010-09-17 Heng Li * put n_smpl to "bcf1_t" to simplify API a little commit | commitdiff | tree | snapshot
2010-09-17 Heng Lifixed a bug in indexing commit | commitdiff | tree | snapshot
2010-09-16 Heng Li * fixed a bug in capQ commit | commitdiff | tree | snapshot
2010-09-16 Heng Li * fixed a bug in razip: -c will delete the input file commit | commitdiff | tree | snapshot
2010-09-16 Heng Li * samtools-0.1.8-14 (r727) commit | commitdiff | tree | snapshot
2010-09-16 Heng Li * added varFilter to vcfutils.pl commit | commitdiff | tree | snapshot
2010-09-15 Heng Li * convert BCF to QCALL input commit | commitdiff | tree | snapshot
2010-09-15 Heng Lidynamic band width in realignment commit | commitdiff | tree | snapshot
2010-09-15 Heng Lifixed a bug in realignment commit | commitdiff | tree | snapshot
2010-09-15 Heng Lifixed a minor issue commit | commitdiff | tree | snapshot
2010-09-14 Heng Lifixed a bug in realignment commit | commitdiff | tree | snapshot
2010-09-14 Heng Liminor changes. It is BUGGY now! commit | commitdiff | tree | snapshot
2010-09-14 Heng Li * aggressive gapped aligner is implemented in calmd. commit | commitdiff | tree | snapshot
2010-09-14 On behalf of... Add svn:ignore properties for generated files that... commit | commitdiff | tree | snapshot
2010-09-13 On behalf of... Add svn:ignore properties listing the generated files. commit | commitdiff | tree | snapshot
2010-09-08 Heng Li * samtools-0.1.8-13 (r715) commit | commitdiff | tree | snapshot
2010-09-03 Heng Liquite a lot changes to the contrast caller, but I still... commit | commitdiff | tree | snapshot
2010-09-03 Heng Li * changed 3.434 to 4.343 (typo!) commit | commitdiff | tree | snapshot
2010-09-02 Heng LiSNP calling from the GL field commit | commitdiff | tree | snapshot
2010-09-01 Heng Lifixed another problem commit | commitdiff | tree | snapshot
2010-09-01 Heng Li * fixed bugs in parsing VCF commit | commitdiff | tree | snapshot
2010-09-01 Heng LiDo not compile _BCF_QUAD by default commit | commitdiff | tree | snapshot
2010-09-01 Heng LiWrite the correct ALT and PL in the SNP calling mode. commit | commitdiff | tree | snapshot
2010-09-01 Heng Limore commands for my own uses commit | commitdiff | tree | snapshot
2010-09-01 Heng LiUtilities for processing VCF commit | commitdiff | tree | snapshot
2010-08-31 Heng Lipreliminary contrast variant caller commit | commitdiff | tree | snapshot
2010-08-31 Heng Liz' and z'' can be calculated commit | commitdiff | tree | snapshot
2010-08-31 Heng Li * rename vcfout.c as call1.c commit | commitdiff | tree | snapshot
2010-08-24 Heng Lifixed a bug in calculating the t statistics commit | commitdiff | tree | snapshot
2010-08-24 Heng Li * samtools-0.1.8-13 (r698) commit | commitdiff | tree | snapshot
2010-08-24 Heng Liadded regularized incomplete beta function commit | commitdiff | tree | snapshot
2010-08-23 Heng Lichange the default correlation coefficient commit | commitdiff | tree | snapshot
2010-08-23 Heng Liprint QUAL as floating numbers commit | commitdiff | tree | snapshot
2010-08-23 Heng Li * samtools-0.1.8-12 (r692) commit | commitdiff | tree | snapshot
2010-08-23 Heng Liremove VCF output in mpileup commit | commitdiff | tree | snapshot
2010-08-23 Heng Li * use the revised MAQ error model for mpileup commit | commitdiff | tree | snapshot
2010-08-20 Heng Liadded revised MAQ error model commit | commitdiff | tree | snapshot
2010-08-18 Heng Liallow to read the prior from the error output. EM itera... commit | commitdiff | tree | snapshot
2010-08-17 Heng Li * write a little more VCF header commit | commitdiff | tree | snapshot
2010-08-17 Heng Liuse float for QUAL commit | commitdiff | tree | snapshot
2010-08-14 Heng Lifaster for large sample size (in principle) commit | commitdiff | tree | snapshot
2010-08-14 Heng Li * a numerically stable method to calculate z_{jk} commit | commitdiff | tree | snapshot
2010-08-12 Heng Lifixed an issue in parsing integer commit | commitdiff | tree | snapshot
2010-08-09 Heng Lido not print refname if file is converted from VCF commit | commitdiff | tree | snapshot
2010-08-09 Heng Li * parse PL commit | commitdiff | tree | snapshot
2010-08-09 Heng Li * fixed a bug in kstrtok@kstring.c commit | commitdiff | tree | snapshot
2010-08-09 Heng Li * improved kstring (added kstrtok) commit | commitdiff | tree | snapshot
2010-08-09 Heng Lihelp messages commit | commitdiff | tree | snapshot
2010-08-09 Heng Liperform single-tail test for ED4 commit | commitdiff | tree | snapshot
2010-08-09 Heng Li * test depth, end distance and HWE commit | commitdiff | tree | snapshot
2010-08-08 Heng Lireimplement incomplete gamma functions. no copy-paste commit | commitdiff | tree | snapshot
2010-08-07 Heng Li * bcftools: add HWE (no testing for now) commit | commitdiff | tree | snapshot
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