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40 lines
1.1 KiB
40 lines
1.1 KiB
#compdef samtools |
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#autoload |
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local curcontext="$curcontext" state line ret=1 |
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local -a _files |
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_arguments -C \ |
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'1: :->cmds' \ |
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'2:: :->args' && ret=0 |
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case $state in |
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cmds) |
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_values "samtools command" \ |
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"view[SAM<->BAM conversion]" \ |
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"sort[sort alignment file]" \ |
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"mpileup[multi-way pileup]" \ |
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"depth[compute the depth]" \ |
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"faidx[index/extract FASTA]" \ |
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"tview[text alignment viewer]" \ |
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"index[index alignment]" \ |
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"idxstats[BAM index stats (r595 or later)]" \ |
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"fixmate[fix mate information]" \ |
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"flagstat[simple stats]" \ |
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"calmd[recalculate MD/NM tags and '=' bases]" \ |
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"merge[merge sorted alignments]" \ |
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"rmdup[remove PCR duplicates]" \ |
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"reheader[replace BAM header]" \ |
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"cat[concatenate BAMs]" \ |
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"bedcov[read depth per BED region]" \ |
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"targetcut[cut fosmid regions (for fosmid pool only)]" \ |
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"phase[phase heterozygotes]" \ |
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"bamshuf[shuffle and group alignments by name]" |
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ret=0 |
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;; |
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*) |
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_files |
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;; |
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esac |
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return ret
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