samtools release 1.20: * 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)