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+#compdef bedtools
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+#autoload
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+
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+local curcontext="$curcontext" state line ret=1
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+local -a _files
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+
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+_arguments -C \
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+ '1: :->cmds' \
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+ '2:: :->args' && ret=0
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+
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+case $state in
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+ cmds)
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+ _values "bedtools command" \
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+ "--contact[Feature requests, bugs, mailing lists, etc.]" \
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+ "--help[Print this help menu.]" \
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+ "--version[What version of bedtools are you using?.]" \
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+ "annotate[Annotate coverage of features from multiple files.]" \
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+ "bamtobed[Convert BAM alignments to BED (& other) formats.]" \
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+ "bamtofastq[Convert BAM records to FASTQ records.]" \
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+ "bed12tobed6[Breaks BED12 intervals into discrete BED6 intervals.]" \
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+ "bedpetobam[Convert BEDPE intervals to BAM records.]" \
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+ "bedtobam[Convert intervals to BAM records.]" \
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+ "closest[Find the closest, potentially non-overlapping interval.]" \
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+ "cluster[Cluster (but don't merge) overlapping/nearby intervals.]" \
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+ "complement[Extract intervals _not_ represented by an interval file.]" \
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+ "coverage[Compute the coverage over defined intervals.]" \
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+ "expand[Replicate lines based on lists of values in columns.]" \
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+ "fisher[Calculate Fisher statistic b/w two feature files.]" \
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+ "flank[Create new intervals from the flanks of existing intervals.]" \
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+ "genomecov[Compute the coverage over an entire genome.]" \
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+ "getfasta[Use intervals to extract sequences from a FASTA file.]" \
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+ "groupby[Group by common cols. & summarize oth. cols. (~ SQL "groupBy")]" \
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+ "igv[Create an IGV snapshot batch script.]" \
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+ "intersect[Find overlapping intervals in various ways.]" \
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+ "jaccard[Calculate the Jaccard statistic b/w two sets of intervals.]" \
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+ "links[Create a HTML page of links to UCSC locations.]" \
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+ "makewindows[Make interval "windows" across a genome.]" \
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+ "map[Apply a function to a column for each overlapping interval.]" \
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+ "maskfasta[Use intervals to mask sequences from a FASTA file.]" \
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+ "merge[Combine overlapping/nearby intervals into a single interval.]" \
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+ "multicov[Counts coverage from multiple BAMs at specific intervals.]" \
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+ "multiinter[Identifies common intervals among multiple interval files.]" \
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+ "nuc[Profile the nucleotide content of intervals in a FASTA file.]" \
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+ "overlap[Computes the amount of overlap from two intervals.]" \
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+ "pairtobed[Find pairs that overlap intervals in various ways.]" \
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+ "pairtopair[Find pairs that overlap other pairs in various ways.]" \
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+ "random[Generate random intervals in a genome.]" \
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+ "reldist[Calculate the distribution of relative distances b/w two files.]" \
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+ "sample[Sample random records from file using reservoir sampling.]" \
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+ "shuffle[Randomly redistrubute intervals in a genome.]" \
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+ "slop[Adjust the size of intervals.]" \
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+ "sort[Order the intervals in a file.]" \
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+ "subtract[Remove intervals based on overlaps b/w two files.]" \
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+ "tag[Tag BAM alignments based on overlaps with interval files.]" \
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+ "unionbedg[Combines coverage intervals from multiple BEDGRAPH files.]" \
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+ "window[Find overlapping intervals within a window around an interval.]" \
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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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+
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+return ret
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