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samtools.git
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
2010-07-22 Heng Li * preliminary multisample SNP caller. commit | commitdiff | tree | snapshot
2010-07-14 Heng Li * samtools-0.1.8-2 (r617) commit | commitdiff | tree | snapshot
2010-07-14 Heng Li * added mutli-sample framework. It is not working... commit | commitdiff | tree | snapshot
2010-07-13 Heng Li * samtools-0.1.8-1 (r615) commit | commitdiff | tree | snapshot
2010-07-12 Heng LiRelease samtools-0.1.8 commit | commitdiff | tree | snapshot
2010-07-12 Heng Lifixed a compiling issue for Windows commit | commitdiff | tree | snapshot
2010-07-12 Heng Lifixed a bug in sorting when output to stdout (by Peter... commit | commitdiff | tree | snapshot
2010-07-09 Heng Lichange the command line option of pileup commit | commitdiff | tree | snapshot
2010-07-09 Heng Limake pileup work with CIGAR with I/D at the beginning... commit | commitdiff | tree | snapshot
2010-07-09 Heng Li * make tview more friendly commit | commitdiff | tree | snapshot
2010-07-08 Heng Li * samtools-0.1.7-r607 commit | commitdiff | tree | snapshot
2010-07-08 Heng Liremoved a debugging example commit | commitdiff | tree | snapshot
2010-07-08 Heng Li * samtools-.1.7-18 (r605) commit | commitdiff | tree | snapshot
2010-07-02 Heng Lifixed a minor bug in idxstats commit | commitdiff | tree | snapshot
2010-06-16 Heng Lifixed a minor bug in indexing commit | commitdiff | tree | snapshot
2010-06-15 Heng Lichange printf() to puts in exporting commit | commitdiff | tree | snapshot
2010-06-14 Heng Liminor fix. No actual effect. commit | commitdiff | tree | snapshot
2010-06-14 Heng Liadded Makefile targets to compile shared/dynamic library commit | commitdiff | tree | snapshot
2010-06-13 Heng Li * samtools-0.1.7-17 (r596) commit | commitdiff | tree | snapshot
2010-06-13 Heng Li * samtools-0.1.7-16 (r595) commit | commitdiff | tree | snapshot
2010-06-13 Heng Lifixed a bug for unmapped sequences in indexing commit | commitdiff | tree | snapshot
2010-06-12 Heng Lirename iterf as iter commit | commitdiff | tree | snapshot
2010-06-12 Heng Li * samtools-0.1.7-15 (r592) commit | commitdiff | tree | snapshot
2010-06-12 Heng Li * samtools-0.1.7-14 (r591) commit | commitdiff | tree | snapshot
2010-06-12 Heng Li * samtools-0.1.7-13 (r590) commit | commitdiff | tree | snapshot
2010-06-12 Heng Li * samtools-0.1.7-12 (r589) commit | commitdiff | tree | snapshot
2010-06-11 Heng Li * samtools-0.1.7-11 (r588) commit | commitdiff | tree | snapshot
2010-06-11 Heng Li * samtools-0.1.7-10 (r587) commit | commitdiff | tree | snapshot
2010-06-11 Heng Li * samtools-0.1.7-9 (r586) commit | commitdiff | tree | snapshot
2010-06-11 Heng Li * samtools-0.1.7-8 (r585) commit | commitdiff | tree | snapshot
2010-06-11 Heng Li * samtools-0.1.7-7 (r584) commit | commitdiff | tree | snapshot
2010-06-11 Petr DanecekInitial release on behalf of Aylwyn Scally commit | commitdiff | tree | snapshot
2010-05-07 Petr DanecekAdded a note about the indels coordinates commit | commitdiff | tree | snapshot
2010-04-23 Petr DanecekAdded the possibility to print or not to print the... commit | commitdiff | tree | snapshot
2010-04-15 Petr DanecekMore descriptive message for space separated tags commit | commitdiff | tree | snapshot
2010-04-14 Petr DanecekSpeedup with -i, no need to query the reference all... commit | commitdiff | tree | snapshot
2010-03-15 Petr DanecekFixed the order of sequences in the header commit | commitdiff | tree | snapshot
2010-03-04 Petr DanecekAdded possibility to select indels only and fixed a... commit | commitdiff | tree | snapshot
2010-02-27 On behalf of... Improve the invalid 'BAM\1' magic number error message... commit | commitdiff | tree | snapshot
2010-02-26 Petr DanecekImproved efficiency of header parsing commit | commitdiff | tree | snapshot
2010-02-24 Heng LiUpdated export2sam.pl by Chris Saunders from Illumina. commit | commitdiff | tree | snapshot
2010-02-17 Petr DanecekFixed filtering of SNPs near indels. Added min indel... commit | commitdiff | tree | snapshot
2010-02-12 Petr DanecekPrint an error for pileups in simple format commit | commitdiff | tree | snapshot
2010-02-11 Heng Liadded a hidden option in pileup to output the base... commit | commitdiff | tree | snapshot
2010-02-09 Petr DanecekAdded possibility to specify a custom column title... commit | commitdiff | tree | snapshot
2010-02-09 Petr DanecekAdded the -d option to limit maximum depth for indels. commit | commitdiff | tree | snapshot
2010-02-03 Petr DanecekAdded VCF header commit | commitdiff | tree | snapshot
2010-02-01 Heng Li * samtools-0.1.7-6 commit | commitdiff | tree | snapshot
2010-01-11 On behalf of... Put the right filename in the error message. commit | commitdiff | tree | snapshot
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