X-Git-Url: https://src.twobees.de/?a=blobdiff_plain;ds=sidebyside;f=stow%2Foh-my-zsh%2F.oh-my-zsh%2Fplugins%2Fbedtools%2F_bedtools;fp=stow%2Foh-my-zsh%2F.oh-my-zsh%2Fplugins%2Fbedtools%2F_bedtools;h=0000000000000000000000000000000000000000;hb=1a8e170bbe5c6641a26ab1ce2e6ce6c5c1faa4cd;hp=ef6c4179afc7125390fb1a0ae96c03f0fb4acb3c;hpb=475ba35502579302593f4735c853c49ef1845dcb;p=dotfiles.git diff --git a/stow/oh-my-zsh/.oh-my-zsh/plugins/bedtools/_bedtools b/stow/oh-my-zsh/.oh-my-zsh/plugins/bedtools/_bedtools deleted file mode 100644 index ef6c417..0000000 --- a/stow/oh-my-zsh/.oh-my-zsh/plugins/bedtools/_bedtools +++ /dev/null @@ -1,64 +0,0 @@ -#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