samtools-patched
A copy of samtools (from samtools.sf.net) with lots of patches:
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Enhanced filter syntax for 'samtools view'. The '-f' and 'F' switches not take the same mnemonic codes as those used in the output. In addition, the XF tagged field contains more flags, we use 1(m) for merged and 2(t) for adapter-trimmed reads, Filtering on the sequence length is also possible ('-m' or '-M').
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More statistics in 'samtools flagstat'. Also, the same statistics are available in table form per read-group through 'samtools flagstatx'.
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The new command 'samtools covstat' tallies coverage of the target by read-group and by target sequence.
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'samtools view' can produce FastQ as output format. Alignments are not included, but most common conventions are followed. (This code avoids producing special characters at the beginning of quality line to make life easier for weak FastQ parsers. Please don't use FastQ if you have the choice.)
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Cleaner handling of read groups in commands that respect them. Single characters are generally allowed as valid read groups.
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More error checking and reporting, especially on out-of-disk-space conditions.