samtools release 1.13: * Fixed samtools view FILE REGION, mpileup -r REGION, coverage -r REGION and other region queries: fixed bug introduced in 1.12, which led to region queries producing very few reads for some queries (especially for larger target regions) when unmapped reads were present. Thanks to `@vinimfava` (#1451), `@JingGuo1997` (#1457) and Ramprasad Neethiraj (#1460) for reporting the respective issues. * Added options to set and clear flags to samtools view. Along with the existing remove aux tags this gives the ability to remove mark duplicate changes (part of #1358) (#1441) * samtools view now has long option equivalents for most of its single-letter options. Thanks to John Marshall. (#1442) * A new tool, samtools import, has been added. It reads one or more FASTQ files and converts them into unmapped SAM, BAM or CRAM. (#1323) * Fixed samtools coverage error message when the target region name is not present in the file header. Thanks to `@Lyn16` for reporting it. (#1462; fixes #1461) * Made samtools coverage ASCII mode produce true ASCII output. Previously it would produce UTF-8 characters. (#1423; fixes #1419) * samtools coverage now allows setting the maximum depth, using the -d/--depth option. Also, the default maximum depth has been set to 1000000. (#1415; fixes #1395) * Complete rewrite of samtools depth. This means it is now considerably faster and does not need a depth limit to avoid high memory usage. Results should mostly be the same as the old command with the potential exception of overlap removal. (#1428; fixes #889, helps ameliorate #1411) * samtools flags now accepts any number of command line arguments, allowing multiple SAM flag combinations to be converted at once. Thanks to John Marshall. (#1401, fixes #749) * samtools ampliconclip, ampliconstats and plot-ampliconstats now support inputs that list more than one reference. (#1410 and #1417; fixes #1396 and #1418) * samtools ampliconclip now accepts the --tolerance option, which allows the user to set the number of bases within which a region is matched. The default is 5. (#1456) * Updated the documentation on samtools ampliconclip to be clearer about what it does. From a suggestion by Nathan S Watson-Haigh. (#1448) * Fixed negative depth values in ampliconstats output. (#1400) * samtools addreplacerg now allows for updating (replacing) an existing `@RG` line in the output header, if a new `@RG` line is provided in the command line, via the -r argument. The update still requires the user's approval, which can be given with the new -w option. Thanks to Chuang Yu. (#1404) * Stopped samtools cat from outputting multiple CRAM EOF markers. (#1422) * Three new counts have been added to samtools flagstat: primary, mapped primary and duplicate primary. (#1431; fixes #1382) * samtools merge now accepts a `-o FILE` option specifying the output file, similarly to most other subcommands. The existing way of specifying it (as the first non-option argument, alongside the input file arguments) remains supported. Thanks to David McGaughey and John Marshall. (#1434) * The way samtools merge checks for existing files has been changed so that it does not hang when used on a named pipe. (#1438; fixes #1437) * Updated documentation on mpileup to highlight the fact that the filtering options on FLAGs work with ANY rules. (#1447; fixes #1435) * samtools can now be configured to use a copy of HTSlib that has been set up with separate build and source trees. When this is the case, the `--with-htslib` configure option should be given the location of the HTSlib build tree. (Note that samtools itself does not yet support out-of-tree builds). Thanks to John Marshall. (#1427; companion change to samtools/htslib#1277)