From 9b32fadfe3c215496ac5319840b94896af1c7028 Mon Sep 17 00:00:00 2001 From: Rolf Schroeder Date: Thu, 12 Feb 2015 08:51:50 +0100 Subject: [PATCH] Add init impl of bedtools completion --- plugins/bedtools/_bedtools | 64 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 plugins/bedtools/_bedtools diff --git a/plugins/bedtools/_bedtools b/plugins/bedtools/_bedtools new file mode 100644 index 00000000..ef6c4179 --- /dev/null +++ b/plugins/bedtools/_bedtools @@ -0,0 +1,64 @@ +#compdef bedtools +#autoload + +local curcontext="$curcontext" state line ret=1 +local -a _files + +_arguments -C \ + '1: :->cmds' \ + '2:: :->args' && ret=0 + +case $state in + cmds) + _values "bedtools command" \ + "--contact[Feature requests, bugs, mailing lists, etc.]" \ + "--help[Print this help menu.]" \ + "--version[What version of bedtools are you using?.]" \ + "annotate[Annotate coverage of features from multiple files.]" \ + "bamtobed[Convert BAM alignments to BED (& other) formats.]" \ + "bamtofastq[Convert BAM records to FASTQ records.]" \ + "bed12tobed6[Breaks BED12 intervals into discrete BED6 intervals.]" \ + "bedpetobam[Convert BEDPE intervals to BAM records.]" \ + "bedtobam[Convert intervals to BAM records.]" \ + "closest[Find the closest, potentially non-overlapping interval.]" \ + "cluster[Cluster (but don't merge) overlapping/nearby intervals.]" \ + "complement[Extract intervals _not_ represented by an interval file.]" \ + "coverage[Compute the coverage over defined intervals.]" \ + "expand[Replicate lines based on lists of values in columns.]" \ + "fisher[Calculate Fisher statistic b/w two feature files.]" \ + "flank[Create new intervals from the flanks of existing intervals.]" \ + "genomecov[Compute the coverage over an entire genome.]" \ + "getfasta[Use intervals to extract sequences from a FASTA file.]" \ + "groupby[Group by common cols. & summarize oth. cols. (~ SQL "groupBy")]" \ + "igv[Create an IGV snapshot batch script.]" \ + "intersect[Find overlapping intervals in various ways.]" \ + "jaccard[Calculate the Jaccard statistic b/w two sets of intervals.]" \ + "links[Create a HTML page of links to UCSC locations.]" \ + "makewindows[Make interval "windows" across a genome.]" \ + "map[Apply a function to a column for each overlapping interval.]" \ + "maskfasta[Use intervals to mask sequences from a FASTA file.]" \ + "merge[Combine overlapping/nearby intervals into a single interval.]" \ + "multicov[Counts coverage from multiple BAMs at specific intervals.]" \ + "multiinter[Identifies common intervals among multiple interval files.]" \ + "nuc[Profile the nucleotide content of intervals in a FASTA file.]" \ + "overlap[Computes the amount of overlap from two intervals.]" \ + "pairtobed[Find pairs that overlap intervals in various ways.]" \ + "pairtopair[Find pairs that overlap other pairs in various ways.]" \ + "random[Generate random intervals in a genome.]" \ + "reldist[Calculate the distribution of relative distances b/w two files.]" \ + "sample[Sample random records from file using reservoir sampling.]" \ + "shuffle[Randomly redistrubute intervals in a genome.]" \ + "slop[Adjust the size of intervals.]" \ + "sort[Order the intervals in a file.]" \ + "subtract[Remove intervals based on overlaps b/w two files.]" \ + "tag[Tag BAM alignments based on overlaps with interval files.]" \ + "unionbedg[Combines coverage intervals from multiple BEDGRAPH files.]" \ + "window[Find overlapping intervals within a window around an interval.]" \ + ret=0 + ;; + *) + _files + ;; +esac + +return ret