samtools/samtools 1.20

on GitHub

Download the source code here: samtools-1.20.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.)

New work and changes:

• Added a --max-depth option to bedcov, for more control over the depth limit used when calculating the pileup. Previously this limit was set at 64000; now it is set to over 2 billion, so effectively all bases will be counted. (PR #1970, fixes #1950. Reported by ellisjj)

• Added mpileup --output-extra RLEN to display the unclipped read length. (PR #1971, feature request #1959. Requested by Feng Tian)

• Improved checking of symbolic flag names (e.g. UNMAP) passed to samtools. (PR #1981, fixes #1977. Reported by Ilya Shlyakhter)

• The samtools consensus --min-depth option now works for the Bayesian mode as well as the simple one. (PR #1989, feature request #1982. Requested by Gautier Richard)

• It's now possible to use the samtools fastq -d tag:val option multiple times, allowing matches on more than one tag/value. It also gets a -D option which allows the values to be listed in a file. (PR #1993, feature request #1958. Requested by Tristan Lefebure)

• Added samtools fixmate -M option to sanity check base modification (ML, MM, MN) tags, and where necessary adjust modification data on hard-clipped records. (PR #1990)

• Made mpileup run faster. (PR #1995)

• samtools import now adds a @PG header to the files it makes. As with other sub-commands, this can be disabled by using --no-PG. (PR #2008. Requested by Steven Leonard)

• The samtools split -d option to split by tag value now works on tags with integer values. (PR #2005, feature request #1956. Requested by Alex Leonard)

• Adjusted samtools sort -n (by name) so that primary reads are always sorted before secondary / supplementary. (PR #2012, feature request #2010. Requested by Stijn van Dongen)

• Added samtools bedcov -H option to print column headers in the output. (PR #2025. Thanks to Dr. K. D. Murray)

Documentation:

• Added a note that BAQ is applied before filtering and overlap removal during mpileup processing. (PR #1988, fixes #1985. Reported by Joseph Galasso)

• Added 3.1 to the list of supported CRAM versions in the samtools manual page. (PR #2009. Thanks to Andrew Thrasher)

• Made assorted improvements to ampliconclip, flagstat and markdup manual pages. (PR #2014)

Bug Fixes:

• Security fix: Fixed double free that could occur if bed file indexing failed due to running out of memory. This bug first appeared in version 1.19.1. (PR #2026)

• Corrected error message printed when faidx fails to load the fai index. (PR #1987. Thanks to Nick Moore)

• Fixed bug introduced in release 1.4 that caused incorrect reference bases to be printed by samtools mpileup -a -f ref.fa in the zero-depth regions at the end of each reference. (PR #2019, fixes #2018. Reported by Joe Georgeson)

• Fixed a samtools view usage crash on MinGW when given invalid options. (PR #2030, fixes #2029. Reported by Divon Lan)

Non user-visible changes and build improvements:

• Added tests to ensure that CRAM compression is working properly. (PR #1969, part of fix for #1968. Reported by Clockris)