Date: Sun, 29 Jul 2018 23:28:01 +0000 From: bugzilla-noreply@freebsd.org To: ports-bugs@FreeBSD.org Subject: [Bug 230171] biology/samtools: Update to 1.9 Message-ID: <bug-230171-7788@https.bugs.freebsd.org/bugzilla/>
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D230171 Bug ID: 230171 Summary: biology/samtools: Update to 1.9 Product: Ports & Packages Version: Latest Hardware: Any OS: Any Status: New Severity: Affects Only Me Priority: --- Component: Individual Port(s) Assignee: ports-bugs@FreeBSD.org Reporter: ndowens.fbsd@yandex.com CC: cartwright@asu.edu CC: cartwright@asu.edu Flags: maintainer-feedback?(cartwright@asu.edu) Created attachment 195616 --> https://bugs.freebsd.org/bugzilla/attachment.cgi?id=3D195616&action= =3Dedit Update Samtools mpileup VCF and BCF output is now deprecated. It is still function= al, but will warn. Please use bcftools mpileup instead. (#884) Samtools mpileup now handles the '-d' max_depth option differently. The= re 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 nu= mber 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 read= s. (#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 prima= ry 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 rad= ix sort. (#835, thanks to Zhuravleva Aleksandra) Samtools idxstats now works on SAM and CRAM files, however this isn't f= ast due to some information lacking from indices. (#832) Compression levels may now be specified with the level=3DN output-fmt-o= ption. E.g. with -O bam,level=3D3. Various documentation improvements. Bug-fixes: Improved error reporting in several places. (#827, #834, #877, cd71= 97) 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 '=3D' and 'X' CIGAR operators when counti= ng 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, reporte= d 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 t= ake 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 mismatche= s). (#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 recor= ds where the sequence is absent. --=20 You are receiving this mail because: You are the assignee for the bug.=
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