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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
2010-08-06 Heng Li * Special functions: log(gamma()), erfc(), P(a,x)... commit | commitdiff | tree | snapshot
2010-08-06 Heng LiFisher's exact test commit | commitdiff | tree | snapshot
2010-08-06 Heng Li * samtools-0.1.8-11 (r672) commit | commitdiff | tree | snapshot
2010-08-05 Heng Li * the code base is stablized again. commit | commitdiff | tree | snapshot
2010-08-05 Heng Liminor commit | commitdiff | tree | snapshot
2010-08-05 Heng Liunfinished vcf parser commit | commitdiff | tree | snapshot
2010-08-05 Heng Li * added prelimiary VCF parser (not finished) commit | commitdiff | tree | snapshot
2010-08-04 Heng Li * allow to set min base q commit | commitdiff | tree | snapshot
2010-08-04 Heng Lispec commit | commitdiff | tree | snapshot
2010-08-04 Heng Liadded more examples commit | commitdiff | tree | snapshot
2010-08-04 Heng Lifixed compilation error commit | commitdiff | tree | snapshot
2010-08-04 Heng Limove bcftools to samtools commit | commitdiff | tree | snapshot
2010-08-03 Heng Lifixed another minor bug commit | commitdiff | tree | snapshot
2010-08-03 Heng Li * samtools-0.1.8-10 (r658) commit | commitdiff | tree | snapshot
2010-08-03 Heng Li * fixed a bug commit | commitdiff | tree | snapshot
2010-08-02 Heng Limissing a column in VCF output... commit | commitdiff | tree | snapshot
2010-08-02 Heng Lifixed a memory leak commit | commitdiff | tree | snapshot
2010-08-02 Heng Lifixed a bug in bcf reader commit | commitdiff | tree | snapshot
2010-08-02 Heng Lifixed a bug commit | commitdiff | tree | snapshot
2010-08-02 Heng Li * samtools-0.1.8-9 (r649) commit | commitdiff | tree | snapshot
2010-08-02 Heng LiGenerate binary VCF commit | commitdiff | tree | snapshot
2010-07-28 Heng Li * samtools-0.1.8-8 (r644) commit | commitdiff | tree | snapshot
2010-07-28 Heng Li * fixed a STUPID bug, which cost me a lot of time. commit | commitdiff | tree | snapshot
2010-07-28 Heng Lisupposedly this is THE correct implementation, but... commit | commitdiff | tree | snapshot
2010-07-28 Heng LiNOT ready yet. Going to make further changes... commit | commitdiff | tree | snapshot
2010-07-26 Heng Li * samtools-0.1.8-7 (r639) commit | commitdiff | tree | snapshot
2010-07-25 Heng Li * samtools-0.1.8-6 (r638) commit | commitdiff | tree | snapshot
2010-07-24 Heng Liminor changes commit | commitdiff | tree | snapshot
2010-07-24 Heng Liminor tweaks commit | commitdiff | tree | snapshot
2010-07-24 Heng Liposterior expectation FINALLY working. I am so tired... commit | commitdiff | tree | snapshot
2010-07-23 Heng Lianother minor fix to mpileup commit | commitdiff | tree | snapshot
2010-07-23 Heng Liadded the format column commit | commitdiff | tree | snapshot
2010-07-23 Heng Liadded an alternative prior commit | commitdiff | tree | snapshot
2010-07-23 Heng Licalculate posterior allele frequency commit | commitdiff | tree | snapshot
2010-07-23 Heng Li * samtools-0.1.8-3 (r627) commit | commitdiff | tree | snapshot
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