Release 1.20 created by Rob Davies on 15 April 2024, 14:24:33 UTC
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) -----BEGIN PGP SIGNATURE----- iQJJBAABCgAzFiEEaGn1wQ1nqxSLDC2XHsvluhXGTMwFAmYdOKEVHHJtZCtnaXRA c2FuZ2VyLmFjLnVrAAoJEB7L5boVxkzMpY4P+gLQVf5Z3T9MAjvStn4YvX/vmmnf HI1mbc9yO7SknzyvRFCx2CsaXB4uKMNK23Lx92GqqcmUdRN1yhxunhaB3eJ+azlM kKIo3QAcso0GbAdaHEg8+E5Fg+Y8f21bBOY66EnQOUB/aChcE+w8D8/t8ZyRezjn 4TuYC9R4AHcAMlQVnik9jtTtLDcCqk/yScJfOvQIDslVHkhRbm6eGMiyN5Nwtlr0 LYrp17tU5Ry8b/7gvhoB0UKR81jTHT5rIbgZQl4VXwKcdG9IBc0gbFMSNNfDXJa5 RxhQLe3PB5Ru24BMviwIvF2iAlKYKFXFXFZoEhiGN8d0ThZbFppInCrSX2/tCC8c j7slRmrJUIa8fE2KChQfXtr+ApuUNN7QdM8y7DfhkgfA7fWM0E3GB7U9sNL6/74i /IJ++5nhOf/JIYDtrTk2KRuNhpjDkrVmva8u9PfLbIIjTgknq74O6CoAl6oCfxZ0 Ci4DlfhVWvvXvOT1W//U+PCG+QhSGd1i5Twem5gi8U4p6jsQvllnAXwUe+EDEM/M fn7wSz7fA0szH3nW+z19TxSZJrGYPxa72Lz4HULUG+URoYNuAK4QlDwcHvKekft6 hMpq0rkRYrjZXH6z1Bn7G9cH4hE/ip8diyN026cr5FLNpxa8XuQBeFHhIyN7H3VF MgqwPr/QACip0GIy =ZNS1 -----END PGP SIGNATURE-----
Target: 906a3b562ef985d2a9777768f8a81001d6ce6dcb
Directory: 882afd974bda060a076bc03f2fe87e559778f61a
Directory: 882afd974bda060a076bc03f2fe87e559778f61a
