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.