Release 1.9 created by Rob Davies on 18 July 2018, 08:47:01 UTC
samtools release 1.9:
* 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. -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) iQIcBAABAgAGBQJbTv6FAAoJEB7L5boVxkzM+9YP/3YhdKt04OZxOvwpkLwyTkSL T9YAizISciF87Nej6WRo4hfY5NsXDwtREIBOON+mWWeARmHH/ysOSJOr+ZZNpgVl bJCo4CPXoNRp4lXbZkLnHyUnisY4nilZOzhIJC1f0cjEenvv5Sr7sEb6ePp1s1HX FBDdWzmL3DLfTBGsyU34Xd7bKbrGzD4YPL8X2iTGUNc/ebsF6D8PwwkKYOF8k29z GjBRRKeFkBKJphtHm/zDw34jLYrBLGsBG1GbHJK3nZVvgRpCO3Y7C6QGR7emY72Z 9W1vEcinjTnFWYl6x1L+yCY758lIdEEFTK59YtcA/YK3UlgYgHObOJFXyjM/ZBFL sDhSzVbv7SPQIhTqPjcuLUmrr3SaH9MAdYJJ00LaC1r+fnAtfSSEcjOp2nGVf3xa /+JoKkqP9vi5aho4mAJU3G8Hk26daS+VGMOdgvz68bdaInSu034xEnZH4dW2/SRu 23xcsB071LmXg62hwtc7wmCT4uy/G81mnur/O1vCfsSkMUkxB7DgZl2e8t32Oc64 X+1ycXnT3IOZSmMZP0hziDNBKaJK43cdbPW9gwYKtL9dbeEX/TQIyjmaNKQSskY5 djb2fA5RdVWqQw6UKkGRFlHnY1NMst+prpouJvB0vugRw4yIj7oCORYMlI0P/eps ERymPASFnwefiIJJYU7n =VqVc -----END PGP SIGNATURE-----
Target: b24d8121509cdfc745d73dd3b90da5571a6d4db9
Directory: 07d43c842504e9ed676f62bb48e5b864b441cbaa
Directory: 07d43c842504e9ed676f62bb48e5b864b441cbaa
