samtools release 1.15: Notice: * Samtools mpileup VCF and BCF output (deprecated in release 1.9) has been removed. Please use bcftools mpileup instead. New work and changes: * Added "--min-BQ" and "--min-MQ" options to "depth". These match the equivalent long options found in "samtools mpileup" and gives a consistent way of specifying the base and mapping quality filters. (#1584; fixes #1580. Reported by Chang Y) * Improved automatic file type detection with "view -u" or "view -1". Setting either of these options would default to BAM format regardless of the usual automatic file type selection based on the file name. The defaults are now only used when the file name does not indicate otherwise. (#1582) * For "markdup" optical duplicate marking add regex options for custom coordinates. For the case of non standard read names (QNAME), add options to read the coordinates and, optionally, another part of the string to test for optical duplication. (#1558) * New "samtools consensus" subcommand for generating consensus from SAM, BAM or CRAM files based on the contents of the alignment records. The consensus is written as FASTA, FASTQ or as a pileup oriented format. The default FASTA/FASTQ output includes one base per non-gap consensus, with insertions with respect to the aligned reference being included and deletions removed. This could be used to compute a new reference from sequence assemblies to realign against. (#1557) * New "samtools view --fetch-pairs" option. This options retrieves pairs even when the mate is outside of the requested region. Using this option enables the multi-region iterator and a region to search must be specified. The input file must be an indexed regular file. (#1542) * Building on #1530 below, add a tview reflist for Goto. (#1539, thanks to Adam Blanchet) * Completion of references added to tview Goto. (#1530; thanks to Adam Blanchet) * New "samtools head" subcommand for conveniently displaying the headers of a SAM, BAM, or CRAM file. Without options, this is equivalent to `samtools view --header-only --no-PG` but more succinct and memorable. (#1517; thanks to John Marshall) Bug Fixes: * Free memory when stats fails to read the header of a file. (#1592; thanks to Mathias Schmitt) * Fixed empty field on unsupported aux tags in "mpileup --output-extra". Replaces the empty fields on unsupported aux tags with a '*'. (#1553; fixes #1544. Thanks to Adam Blanchet) * In mpileup, the --output-BP-5 and --output-BP are no longer mutually exclusive. This fixes the problem of output columns being switched. (#1540; fixes 1534. Reported by Konstantin Riege) * Fix for hardclip bug in ampliconclip. Odd length sequences resulted in random characters appearing in sequence. (#1538; fixes #1527. Reported by Ivana Mihalek) Documentation: * Improved mpileup documentation. (#1566; fixes #1564. Reported by Chang Y) * Fixed "samtools depth -J" documentation, which was reversed. (#1552; fixes #1549. Reported by Stephan Hutter) * Numerous minor man page fixes. (#1528, #1536, #1579, #1590. Thanks to John Marshall for some of these) Non user-visible changes and build improvements: * Replace CentOS test build with Rocky Linux. The CentOS Docker images that our test build depended on has stopped working. Switched to Rocky Linux as the nearest available equivalent. (#1589) * Fix missing autotools on Appveyor. Newer versions of msys2 removed autotools from their base-devel package. This is putting them back. (#1575) * Fixed bug detected by clang-13 with -Wformat-security. (#1553) * Switch to using splaysort in bam_lpileup. Improves speed and efficiency in "tview". (#1548; thanks to Adam Blanchet)