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@daviesrob daviesrob released this Jul 18, 2018 · 58 commits to develop since this release

The samtools-1.9.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.


  • Samtools mpileup VCF and BCF output is now deprecated. It is still functional, but will warn. Please use bcftools mpileup instead. (#884)

  • Samtools mpileup now handles the '-d' max_depth option differently. There is no longer an enforced minimum, and '-d 0' is interpreted as limitless (no maximum - warning this may be slow). The default per-file depth is now 8000, which matches the value mpileup used to use when processing a single sample. To get the previous default behaviour use the higher of 8000 divided by the number of samples across all input files, or 250. (#859)

  • Samtools stats new features:

    • The '--remove-overlaps' option discounts overlapping portions of templates when computing coverage and mapped base counting. (#855)

    • When a target file is in use, the number of bases inside the target is printed and the percentage of target bases with coverage above a given threshold specified by the '--cov-threshold' option. (#855)

    • Split base composition and length statistics by first and last reads. (#814, #816)

  • Samtools faidx new features:

    • Now takes long options. (#509, thanks to Pierre Lindenbaum)

    • Now warns about zero-length and truncated sequences due to the requested range being beyond the end of the sequence. (#834)

    • Gets a new option (--continue) that allows it to carry on when a requested sequence was not in the index. (#834)

    • It is now possible to supply the list of regions to output in a text file using the new '--region-file' option. (#840)

    • New '-i' option to make faidx return the reverse complement of the regions requested. (#878)

    • faidx now works on FASTQ (returning FASTA) and added a new fqidx command to index and return FASTQ. (#852)

  • Samtools collate now has a fast option '-f' that only operates on primary pairs, dropping secondary and supplementary. It tries to write pairs to the final output file as soon as both reads have been found. (#818)

  • Samtools bedcov gets a new '-j' option to make it ignore deletions (D) and reference skips (N) when computing coverage. (#843)

  • Small speed up to samtools coordinate sort, by converting it to use radix sort. (#835, thanks to Zhuravleva Aleksandra)

  • Samtools idxstats now works on SAM and CRAM files, however this isn't fast due to some information lacking from indices. (#832)

  • Compression levels may now be specified with the level=N output-fmt-option. E.g. with -O bam,level=3.

  • Various documentation improvements.

  • Bug-fixes:

    • Improved error reporting in several places. (#827, #834, #877, cd7197)

    • Various test improvements.

    • Fixed failures in the multi-region iterator (view -M) when regions provided via BED files include overlaps (#819, reported by Dave Larson).

    • Samtools stats now counts '=' and 'X' CIGAR operators when counting mapped bases. (#855)

    • Samtools stats has fixes for insert size filtering (-m, -i). (#845; #697 reported by Soumitra Pal)

    • Samtools stats -F now longer negates an earlier -d option. (#830)

    • Fix samtools stats crash when using a target region. (#875, reported by John Marshall)

    • Samtools sort now keeps to a single thread when the -@ option is absent. Previously it would spawn a writer thread, which could cause the CPU usage to go slightly over 100%. (#833, reported by Matthias Bernt)

    • Fixed samtools phase '-A' option which was incorrectly defined to take a parameter. (#850; #846 reported by Dianne Velasco)

    • Fixed compilation problems when using C_INCLUDE_PATH. (#870; #817 reported by Robert Boissy)

    • Fixed --version when built from a Git repository. (#844, thanks to John Marshall)

    • Use noenhanced mode for title in plot-bamstats. Prevents unwanted interpretation of characters like underscore in gnuplot version 5. (#829, thanks to M. Zapukhlyak)

    • blast2sam.pl now reports perfect match hits (no indels or mismatches). (#873, thanks to Nils Homer)

    • Fixed bug in fasta and fastq subcommands where stdout would not be flushed correctly if the -0 option was used.

    • Fixed invalid memory access in mpileup and depth on alignment records where the sequence is absent.

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