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intersect
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Find overlapping paired-genomic-loci from two PGL files
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merge
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Merge nearby paired-genomic-loci within a single file and produce a column containing summary statistics requested through passed parameters (-c and -o)
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subtract
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Find parts of paired-genomic-loci from a PGL file that do not overlap another PGL file
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window
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Filter a PGL file to a particular genomic region
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samTopgl
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Converts a sam file to a PGL file
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coverage
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Find the coverage of a PGL file on another PGL file; usually used to find the coverage of reads from a PGL file derived from a sam file on a set of PGLs. The paired-genomic-loci from file 2 only need to overlap the paired-genomic-loci from file 1.
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closest
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Find the closest paired-genomic-loci from a PGL file for each paired-genomic-loci in another PGL file
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expand
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Expand both loci by a given size
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intersect1D
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Find the paired-genomic-loci that overlap regions from a bed file
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closest1D
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Find the closest paired-genomic-loci to a set of regions from a bed file
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subtract1D
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Find the parts of paired-genomic-loci that do not overlap regions from a bed file
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sort
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Sorts a PGL file for use with other PGLtools operations
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formatbedpe
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Convert a bedpe-like file to a PGL file
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formatTripSparse
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Convert a triplet sparse matrix file set to a PGL file
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conveRt
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Formats the PGL file for use with the GenomicInteractions R package
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browser
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Format a PGL file to be viewed in the UCSC Genome Browser
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juicebox
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Format a PGL file to be viewed in juicebox
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condense
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Convert a PGL file to a BED file with two entries for each PGL entry.
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findLoops
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Convert a PGL file to a BED file with an entry containing the region from the start of anchor A to the stop of anchor B for intra-chromosomal PGLs, and an entry for each anchor for inter-chromosomal PGLs.
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