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Reverted to the previous behaviour, the unmapped reads are not removed. Added -r...
[samtools.git] / misc /
2012-04-24 Petr Danecekinit_regions: check for non-matching sequence names tree | commitdiff
2012-04-23 Petr DanecekResolved merge conflict tree | commitdiff
2012-04-23 Petr DanecekIndexed access can be now combined with target regions... tree | commitdiff
2012-04-17 Heng Lichange getline() to mygetline() tree | commitdiff
2012-04-12 Petr DanecekAdded check for out-of-bounds indels at the end of... tree | commitdiff
2012-04-04 Petr DanecekRemoved glibc dependency (getline) tree | commitdiff
2012-04-04 Petr DanecekMerge remote branch 'main/master' tree | commitdiff
2012-03-29 Heng LiMerge branch 'master' of github.com:samtools/samtools... tree | commitdiff
2012-03-29 samtoolsMerge pull request #2 from peterjc/depad tree | commitdiff
2012-03-29 Petr DanecekCompile cleanly from top-level Makefile. Check for... tree | commitdiff
2012-03-29 Petr DanecekCompile cleanly from top-level Makefile. Check for... tree | commitdiff
2012-03-28 Petr DanecekAdded rule for bamcheck creation tree | commitdiff
2012-03-28 Petr DanecekAdded rule for bamcheck creation tree | commitdiff
2012-03-27 Petr DanecekInitial release of bamcheck and plot-bamcheck tree | commitdiff
2012-03-27 Petr DanecekInitial release of bamcheck and plot-bamcheck tree | commitdiff
2012-03-24 Heng Limove seqtk to a separate project tree | commitdiff
2012-03-09 Heng LiTwo auxilary Lua scripts tree | commitdiff
2011-09-28 Heng Liunpadded output tree | commitdiff
2011-09-23 Heng Liadded the ace2sam converter tree | commitdiff
2011-09-02 Heng Li * Updated samtools to the latest tree | commitdiff
2011-03-18 Heng Liexport2sam.pl-2.3.1, provided by Chris Saunders from... tree | commitdiff
2010-11-15 Heng Li * samtools-0.1.9-16 (r822) tree | commitdiff
2010-10-01 Heng LiI am changing the gap open probability back to 0.001... tree | commitdiff
2010-10-01 Heng Li * samtools-0.1.8-17 (r760) tree | commitdiff
2010-09-16 Heng Li * added varFilter to vcfutils.pl tree | commitdiff
2010-07-13 Heng Li * samtools-0.1.8-1 (r615) tree | commitdiff
2010-07-08 Heng Liremoved a debugging example tree | commitdiff
2010-07-02 Heng Lifixed a minor bug in idxstats tree | commitdiff
2010-06-11 Heng Li * samtools-0.1.7-7 (r584) tree | commitdiff
2010-06-11 Petr DanecekInitial release on behalf of Aylwyn Scally tree | commitdiff
2010-04-23 Petr DanecekAdded the possibility to print or not to print the... tree | commitdiff
2010-04-14 Petr DanecekSpeedup with -i, no need to query the reference all... tree | commitdiff
2010-03-04 Petr DanecekAdded possibility to select indels only and fixed a... tree | commitdiff
2010-02-24 Heng LiUpdated export2sam.pl by Chris Saunders from Illumina. tree | commitdiff
2010-02-17 Petr DanecekFixed filtering of SNPs near indels. Added min indel... tree | commitdiff
2010-02-12 Petr DanecekPrint an error for pileups in simple format tree | commitdiff
2010-02-09 Petr DanecekAdded possibility to specify a custom column title... tree | commitdiff
2010-02-03 Petr DanecekAdded VCF header tree | commitdiff
2010-02-01 Heng Li * samtools-0.1.7-6 tree | commitdiff
2009-12-11 Petr DanecekSmall fix in VCF format: dot for the empty INFO field tree | commitdiff
2009-12-01 Heng Li * samtools-0.1.7-2 (r520) tree | commitdiff
2009-11-30 On behalf of John... Also clean *.exe (for Cygwin users using this makefile). tree | commitdiff
2009-11-27 Heng Li * samtools-0.1.7-1 (r515) tree | commitdiff
2009-10-18 Heng Liadded a small unitity to parse SRA XML files tree | commitdiff
2009-10-09 Petr DanecekAdded the sam2vcf.pl script. tree | commitdiff
2009-10-02 Heng LiFixed minor bugs in novo2sam.pl (on behalf of Ken Chen... tree | commitdiff
2009-09-28 Heng Li * samtools-0.1.6-7 (r468) tree | commitdiff
2009-08-29 Heng Li * samtools-0.1.5-32 (r449) tree | commitdiff
2009-08-19 Heng Li * samtools-0.1.5-31 (r448) tree | commitdiff
2009-08-07 Heng Li * samtools-0.1.5-26 (r442) tree | commitdiff
2009-08-04 Heng Lifixed a SERIOUS bug in setting 0x20 flag tree | commitdiff
2009-08-04 Heng Lifixed two minor bugs (suggested by Tim M Storm) tree | commitdiff
2009-08-04 Heng Li * samtools-0.1.5-24 (r435) tree | commitdiff
2009-07-31 Heng Li * samtools-0.1.5-18 (r423) tree | commitdiff
2009-07-30 Heng Liconvert BLAT psl to SAM. tree | commitdiff
2009-07-30 Heng Li * samtools-0.1.5-16 (r421) tree | commitdiff
2009-07-29 Heng Lido not set "read 1" if reads are not mapped in the... tree | commitdiff
2009-07-28 Heng Li * samtools-0.1.5-15 (r419) tree | commitdiff
2009-07-24 Heng Liskip @header lines in SAM tree | commitdiff
2009-06-12 Heng Li * no changes to samtools itself tree | commitdiff
2009-06-12 Heng Lifixed minor things in Makefile tree | commitdiff
2009-06-12 Heng Li * updated novoalign converter by Colin Hercus et al. tree | commitdiff
2009-06-12 Heng Li * update Makefile tree | commitdiff
2009-06-12 Heng Li * added zlib-1.2.3 as razip requires that tree | commitdiff
2009-06-12 Heng LiUnfinished tree | commitdiff
2009-06-10 Heng Li * samtools.pl-0.3.2 (r322) tree | commitdiff
2009-06-10 Heng Lifixed a typo tree | commitdiff
2009-06-09 Heng Lijust typo. no real change tree | commitdiff
2009-06-08 Heng Lia little bit code cleanup tree | commitdiff
2009-06-08 Heng Li * samtools.pl-0.3.1 tree | commitdiff
2009-06-08 Heng Li * samtools.pl-0.3.0 tree | commitdiff
2009-06-08 Heng Li * samtools.pl-0.2.3 tree | commitdiff
2009-06-04 Heng Li * samtools.pl-0.2.2 tree | commitdiff
2009-06-03 Heng Li * in snpFilter, suppress non-SNP sites tree | commitdiff
2009-06-01 Heng Li * samtools.pl-0.2.1 tree | commitdiff
2009-06-01 Heng Li * samtools.pl-0.2.0 tree | commitdiff
2009-05-28 Heng LiScript for paired-end pileup, contributed by Stephen... tree | commitdiff
2009-05-21 Heng LiRelease samtools-0.1.4 tree | commitdiff
2009-04-28 Heng Liimprove large file support in compilation tree | commitdiff
2009-04-28 Heng Lifixed various issues about the GNU building scripts tree | commitdiff
2009-04-28 Heng Li * samtools-0.1.3-7 (r246) tree | commitdiff
2009-04-15 Heng Liconvert NCBI-BLASTN to SAM tree | commitdiff
2009-04-14 Heng Li * samtools.pl-0.1.1 tree | commitdiff
2009-04-08 Heng Li * samtools-0.1.2-21 tree | commitdiff
2009-04-08 Heng Limake the script robust to the bugs in SOAP-2.1.7 tree | commitdiff
2009-03-24 Heng Lirename Makefile.std as Makefile. GNU building systerm... tree | commitdiff
2009-03-24 Heng Li * samtools-0.1.2-17 tree | commitdiff
2009-03-12 Heng Li * soap2sam.pl-0.1.2 tree | commitdiff
2009-03-10 Heng Li * samtools-0.1.2-14 tree | commitdiff
2009-03-01 Heng Li * wgsim-0.2.3 tree | commitdiff
2009-02-26 Heng Li * wgsim-0.2.2 tree | commitdiff
2009-02-26 Heng Li * wgsim-0.2.1 tree | commitdiff
2009-02-26 Heng Li * wgsim: added a note tree | commitdiff
2009-02-26 Heng Li * wgsim-0.2.0 tree | commitdiff
2009-02-17 Heng Li * move indel_filter.pl to samtools.pl tree | commitdiff
2009-02-12 Heng Li * samtools-0.1.2-6 tree | commitdiff
2009-02-11 Heng Lifixed a bug in generating tag AM tree | commitdiff
2009-01-28 Heng LiScript for filtering indel results tree | commitdiff
2009-01-25 Heng Liconvert ZOOM to SAM tree | commitdiff
2009-01-24 Heng Liadd a script to convert novo alignment to SAM tree | commitdiff
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