Download the source code here: samtools-1.13.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.)
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Fixed
samtools view FILE REGION,mpileup -r REGION,coverage -r REGIONand 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)
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samtools view now has long option equivalents for most of its single-letter options. Thanks to John Marshall. (#1442)
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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)
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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)
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Made samtools coverage ASCII mode produce true ASCII output. Previously it would produce UTF-8 characters. (#1423; fixes #1419)
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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)
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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)
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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)
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samtools ampliconclip, ampliconstats and plot-ampliconstats now support inputs that list more than one reference. (#1410 and #1417; fixes #1396 and #1418)
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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)
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Updated the documentation on samtools ampliconclip to be clearer about what it does. From a suggestion by Nathan S Watson-Haigh. (#1448)
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Fixed negative depth values in ampliconstats output. (#1400)
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samtools addreplacerg now allows for updating (replacing) an existing
@RGline in the output header, if a new@RGline 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)
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Three new counts have been added to samtools flagstat: primary, mapped primary and duplicate primary. (#1431; fixes #1382)
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samtools merge now accepts a
-o FILEoption 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)
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Updated documentation on mpileup to highlight the fact that the filtering options on FLAGs work with ANY rules. (#1447; fixes #1435)
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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-htslibconfigure 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)