71 lines
4.2 KiB
Java
71 lines
4.2 KiB
Java
/*
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* Copyright (c) 2012 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.commandline;
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import org.broad.tribble.Feature;
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import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
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import org.broadinstitute.sting.utils.interval.IntervalSetRule;
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import java.util.List;
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public class IntervalArgumentCollection {
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/**
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* Using this option one can instruct the GATK engine to traverse over only part of the genome. This argument can be specified multiple times.
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* One may use samtools-style intervals either explicitly (e.g. -L chr1 or -L chr1:100-200) or listed in a file (e.g. -L myFile.intervals).
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* Additionally, one may specify a rod file to traverse over the positions for which there is a record in the file (e.g. -L file.vcf).
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* To specify the completely unmapped reads in the BAM file (i.e. those without a reference contig) use -L unmapped.
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*/
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@Input(fullName = "intervals", shortName = "L", doc = "One or more genomic intervals over which to operate. Can be explicitly specified on the command line or in a file (including a rod file)", required = false)
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public List<IntervalBinding<Feature>> intervals = null;
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/**
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* Using this option one can instruct the GATK engine NOT to traverse over certain parts of the genome. This argument can be specified multiple times.
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* One may use samtools-style intervals either explicitly (e.g. -XL chr1 or -XL chr1:100-200) or listed in a file (e.g. -XL myFile.intervals).
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* Additionally, one may specify a rod file to skip over the positions for which there is a record in the file (e.g. -XL file.vcf).
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*/
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@Input(fullName = "excludeIntervals", shortName = "XL", doc = "One or more genomic intervals to exclude from processing. Can be explicitly specified on the command line or in a file (including a rod file)", required = false)
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public List<IntervalBinding<Feature>> excludeIntervals = null;
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/**
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* How should the intervals specified by multiple -L or -XL arguments be combined? Using this argument one can, for example, traverse over all of the positions
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* for which there is a record in a VCF but just in chromosome 20 (-L chr20 -L file.vcf -isr INTERSECTION).
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*/
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@Argument(fullName = "interval_set_rule", shortName = "isr", doc = "Indicates the set merging approach the interval parser should use to combine the various -L or -XL inputs", required = false)
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public IntervalSetRule intervalSetRule = IntervalSetRule.UNION;
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/**
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* Should abutting (but not overlapping) intervals be treated as separate intervals?
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*/
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@Argument(fullName = "interval_merging", shortName = "im", doc = "Indicates the interval merging rule we should use for abutting intervals", required = false)
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public IntervalMergingRule intervalMerging = IntervalMergingRule.ALL;
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/**
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* For example, '-L chr1:100' with a padding value of 20 would turn into '-L chr1:80-120'.
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*/
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@Argument(fullName = "interval_padding", shortName = "ip", doc = "Indicates how many basepairs of padding to include around each of the intervals specified with the -L/--intervals argument", required = false)
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public int intervalPadding = 0;
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}
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