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65 lines
3.2 KiB
Text
65 lines
3.2 KiB
Text
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#compdef bedtools
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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 "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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return ret
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