47 lines
1.3 KiB
Plaintext
47 lines
1.3 KiB
Plaintext
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#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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args)
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case $line[1] in
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view|tview)
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_files=(`find . -name \*.sam -o -name \*.bam | grep '\./[^/]*am' | sed 's/\.\///'`)
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[[ -n "$_files" ]] && _values 'configs' $_files
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ret=0
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;;
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esac
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;;
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esac
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return ret
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