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Home / samtools / 1.1
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README.md 2014-09-23 1.2 kB
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samtools-1.1.tar.bz2 2014-09-23 4.5 MB
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bcftools-1.1.tar.bz2 2014-09-23 1.2 MB
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htslib-1.1.tar.bz2 2014-09-23 844.9 kB
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The 1.1 releases of HTSlib, Samtools, and BCFtools are primarily bug-fix releases, including the following notable fixes and new functionality:

  • Samtools fixmate and flagstat now consider supplementary reads
  • Sorting BAM files with thousands of reference contigs now completes in a reasonable amount of time (#260)
  • Fixed samtools idxstats when displaying statistics from indices generated by samtools 0.1.x (#124)
  • Fixed samtools calmd memory leak (#143)
  • Samtools fixmate now only adds a template cigar tag (ct:Z) when requested with -c, and never adds it repeatedly (#276)
  • Regularised script #! directives as #!/usr/bin/env perl etc (#271, #273)
  • Fixed DPR annotation in samtools mpileup
  • New bcftools convert and plugin commands and annotate --rename-chrs option
  • BCFtools norm performance is improved and now averages QUALs and accumulates IDs and FILTERs
  • Improved bcftools filter expressions, query support for IUPAC ambiguity codes, and annotate support for genotype fields
  • Plugins for bcftools have now moved from annotate to the new plugin command

(Numbers in parentheses refer to corresponding issue numbers in the relevant GitHub repository.)

Source: README.md, updated 2014-09-23