]> git.donarmstrong.com Git - samtools.git/shortlog
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2010-09-20 Heng Li * merge files region-by-region. work on small examples...
2010-09-20 Heng Liimprove qstats by checking the alleles as well
2010-09-17 Heng Liconvert UCSC SNP SQL dump to VCF
2010-09-17 Heng Lihapmap2vcf convertor
2010-09-17 Heng Li * added comments
2010-09-17 Heng Li * put n_smpl to "bcf1_t" to simplify API a little
2010-09-17 Heng Lifixed a bug in indexing
2010-09-16 Heng Li * fixed a bug in capQ
2010-09-16 Heng Li * fixed a bug in razip: -c will delete the input file
2010-09-16 Heng Li * samtools-0.1.8-14 (r727)
2010-09-16 Heng Li * added varFilter to vcfutils.pl
2010-09-15 Heng Li * convert BCF to QCALL input
2010-09-15 Heng Lidynamic band width in realignment
2010-09-15 Heng Lifixed a bug in realignment
2010-09-15 Heng Lifixed a minor issue
2010-09-14 Heng Lifixed a bug in realignment
2010-09-14 Heng Liminor changes. It is BUGGY now!
2010-09-14 Heng Li * aggressive gapped aligner is implemented in calmd.
2010-09-14 On behalf of... Add svn:ignore properties for generated files that...
2010-09-13 On behalf of... Add svn:ignore properties listing the generated files.
2010-09-08 Heng Li * samtools-0.1.8-13 (r715)
2010-09-03 Heng Liquite a lot changes to the contrast caller, but I still...
2010-09-03 Heng Li * changed 3.434 to 4.343 (typo!)
2010-09-02 Heng LiSNP calling from the GL field
2010-09-01 Heng Lifixed another problem
2010-09-01 Heng Li * fixed bugs in parsing VCF
2010-09-01 Heng LiDo not compile _BCF_QUAD by default
2010-09-01 Heng LiWrite the correct ALT and PL in the SNP calling mode.
2010-09-01 Heng Limore commands for my own uses
2010-09-01 Heng LiUtilities for processing VCF
2010-08-31 Heng Lipreliminary contrast variant caller
2010-08-31 Heng Liz' and z'' can be calculated
2010-08-31 Heng Li * rename vcfout.c as call1.c
2010-08-24 Heng Lifixed a bug in calculating the t statistics
2010-08-24 Heng Li * samtools-0.1.8-13 (r698)
2010-08-24 Heng Liadded regularized incomplete beta function
2010-08-23 Heng Lichange the default correlation coefficient
2010-08-23 Heng Liprint QUAL as floating numbers
2010-08-23 Heng Li * samtools-0.1.8-12 (r692)
2010-08-23 Heng Liremove VCF output in mpileup
2010-08-23 Heng Li * use the revised MAQ error model for mpileup
2010-08-20 Heng Liadded revised MAQ error model
2010-08-18 Heng Liallow to read the prior from the error output. EM itera...
2010-08-17 Heng Li * write a little more VCF header
2010-08-17 Heng Liuse float for QUAL
2010-08-14 Heng Lifaster for large sample size (in principle)
2010-08-14 Heng Li * a numerically stable method to calculate z_{jk}
2010-08-12 Heng Lifixed an issue in parsing integer
2010-08-09 Heng Lido not print refname if file is converted from VCF
2010-08-09 Heng Li * parse PL
2010-08-09 Heng Li * fixed a bug in kstrtok@kstring.c
2010-08-09 Heng Li * improved kstring (added kstrtok)
2010-08-09 Heng Lihelp messages
2010-08-09 Heng Liperform single-tail test for ED4
2010-08-09 Heng Li * test depth, end distance and HWE
2010-08-08 Heng Lireimplement incomplete gamma functions. no copy-paste
2010-08-07 Heng Li * bcftools: add HWE (no testing for now)
2010-08-06 Heng Li * Special functions: log(gamma()), erfc(), P(a,x)...
2010-08-06 Heng LiFisher's exact test
2010-08-06 Heng Li * samtools-0.1.8-11 (r672)
2010-08-05 Heng Li * the code base is stablized again.
2010-08-05 Heng Liminor
2010-08-05 Heng Liunfinished vcf parser
2010-08-05 Heng Li * added prelimiary VCF parser (not finished)
2010-08-04 Heng Li * allow to set min base q
2010-08-04 Heng Lispec
2010-08-04 Heng Liadded more examples
2010-08-04 Heng Lifixed compilation error
2010-08-04 Heng Limove bcftools to samtools
2010-08-03 Heng Lifixed another minor bug
2010-08-03 Heng Li * samtools-0.1.8-10 (r658)
2010-08-03 Heng Li * fixed a bug
2010-08-02 Heng Limissing a column in VCF output...
2010-08-02 Heng Lifixed a memory leak
2010-08-02 Heng Lifixed a bug in bcf reader
2010-08-02 Heng Lifixed a bug
2010-08-02 Heng Li * samtools-0.1.8-9 (r649)
2010-08-02 Heng LiGenerate binary VCF
2010-07-28 Heng Li * samtools-0.1.8-8 (r644)
2010-07-28 Heng Li * fixed a STUPID bug, which cost me a lot of time.
2010-07-28 Heng Lisupposedly this is THE correct implementation, but...
2010-07-28 Heng LiNOT ready yet. Going to make further changes...
2010-07-26 Heng Li * samtools-0.1.8-7 (r639)
2010-07-25 Heng Li * samtools-0.1.8-6 (r638)
2010-07-24 Heng Liminor changes
2010-07-24 Heng Liminor tweaks
2010-07-24 Heng Liposterior expectation FINALLY working. I am so tired...
2010-07-23 Heng Lianother minor fix to mpileup
2010-07-23 Heng Liadded the format column
2010-07-23 Heng Liadded an alternative prior
2010-07-23 Heng Licalculate posterior allele frequency
2010-07-23 Heng Li * samtools-0.1.8-3 (r627)
2010-07-22 Heng Li * preliminary multisample SNP caller.
2010-07-14 Heng Li * samtools-0.1.8-2 (r617)
2010-07-14 Heng Li * added mutli-sample framework. It is not working...
2010-07-13 Heng Li * samtools-0.1.8-1 (r615)
2010-07-12 Heng LiRelease samtools-0.1.8
2010-07-12 Heng Lifixed a compiling issue for Windows
2010-07-12 Heng Lifixed a bug in sorting when output to stdout (by Peter...
2010-07-09 Heng Lichange the command line option of pileup
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