DiagnoseTargets now outputs a VCF file
- refactored the statistics classes - concurrent callable statuses by sample are now available. Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
This commit is contained in:
Roger Zurawicki
Mauricio Carneiro
parent
719ec9144a
commit
9ece93ae9c
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@ -1,23 +1,25 @@
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/*
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/*
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* Copyright (c) 2009 The Broad Institute
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* Copyright (c) 2012, The Broad Institute
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* Permission is hereby granted, free of charge, to any person
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*
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* obtaining a copy of this software and associated documentation
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* Permission is hereby granted, free of charge, to any person
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* files (the "Software"), to deal in the Software without
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* obtaining a copy of this software and associated documentation
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* restriction, including without limitation the rights to use,
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* files (the "Software"), to deal in the Software without
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* restriction, including without limitation the rights to use,
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* copies of the Software, and to permit persons to whom the
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* Software is furnished to do so, subject to the following
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* copies of the Software, and to permit persons to whom the
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* conditions:
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* Software is furnished to do so, subject to the following
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* The above copyright notice and this permission notice shall be
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* conditions:
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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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* The above copyright notice and this permission notice shall be
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* included in all copies or substantial portions of the Software.
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* * OTHER DEALINGS IN THE SOFTWARE.
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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 THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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*/
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package org.broadinstitute.sting.gatk.walkers.coverage;
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package org.broadinstitute.sting.gatk.walkers.coverage;
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@ -42,40 +44,40 @@ import java.io.PrintStream;
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/**
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/**
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* Emits a data file containing information about callable, uncallable, poorly mapped, and other parts of the genome
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* Emits a data file containing information about callable, uncallable, poorly mapped, and other parts of the genome
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*
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* <p/>
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* <p>
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* <p>
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* A very common question about a NGS set of reads is what areas of the genome are considered callable. The system
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* A very common question about a NGS set of reads is what areas of the genome are considered callable. The system
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* considers the coverage at each locus and emits either a per base state or a summary interval BED file that
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* considers the coverage at each locus and emits either a per base state or a summary interval BED file that
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* partitions the genomic intervals into the following callable states:
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* partitions the genomic intervals into the following callable states:
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* <dl>
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* <dl>
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* <dt>REF_N</dt>
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* <dt>REF_N</dt>
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* <dd>the reference base was an N, which is not considered callable the GATK</dd>
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* <dd>the reference base was an N, which is not considered callable the GATK</dd>
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* <dt>CALLABLE</dt>
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* <dt>PASS</dt>
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* <dd>the base satisfied the min. depth for calling but had less than maxDepth to avoid having EXCESSIVE_COVERAGE</dd>
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* <dd>the base satisfied the min. depth for calling but had less than maxDepth to avoid having EXCESSIVE_COVERAGE</dd>
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* <dt>NO_COVERAGE</dt>
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* <dt>NO_COVERAGE</dt>
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* <dd>absolutely no reads were seen at this locus, regardless of the filtering parameters</dd>
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* <dd>absolutely no reads were seen at this locus, regardless of the filtering parameters</dd>
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* <dt>LOW_COVERAGE</dt>
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* <dt>LOW_COVERAGE</dt>
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* <dd>there were less than min. depth bases at the locus, after applying filters</dd>
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* <dd>there were less than min. depth bases at the locus, after applying filters</dd>
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* <dt>EXCESSIVE_COVERAGE</dt>
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* <dt>EXCESSIVE_COVERAGE</dt>
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* <dd>more than -maxDepth read at the locus, indicating some sort of mapping problem</dd>
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* <dd>more than -maxDepth read at the locus, indicating some sort of mapping problem</dd>
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* <dt>POOR_MAPPING_QUALITY</dt>
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* <dt>POOR_MAPPING_QUALITY</dt>
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* <dd>more than --maxFractionOfReadsWithLowMAPQ at the locus, indicating a poor mapping quality of the reads</dd>
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* <dd>more than --maxFractionOfReadsWithLowMAPQ at the locus, indicating a poor mapping quality of the reads</dd>
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* </dl>
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* </dl>
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* </p>
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* </p>
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*
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* <p/>
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* <h2>Input</h2>
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* <h2>Input</h2>
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* <p>
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* <p>
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* A BAM file containing <b>exactly one sample</b>.
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* A BAM file containing <b>exactly one sample</b>.
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* </p>
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* </p>
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*
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* <p/>
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* <h2>Output</h2>
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* <h2>Output</h2>
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* <p>
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* <p>
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* <ul>
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* <ul>
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* <li>-o: a OutputFormatted (recommended BED) file with the callable status covering each base</li>
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* <li>-o: a OutputFormatted (recommended BED) file with the callable status covering each base</li>
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* <li>-summary: a table of callable status x count of all examined bases</li>
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* <li>-summary: a table of callable status x count of all examined bases</li>
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* </ul>
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* </ul>
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* </p>
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* </p>
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*
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* <p/>
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* <h2>Examples</h2>
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* <h2>Examples</h2>
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* <pre>
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* <pre>
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* -T CallableLociWalker \
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* -T CallableLociWalker \
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@ -83,31 +85,31 @@ import java.io.PrintStream;
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* -summary my.summary \
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* -summary my.summary \
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* -o my.bed
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* -o my.bed
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* </pre>
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* </pre>
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*
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* <p/>
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* would produce a BED file (my.bed) that looks like:
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* would produce a BED file (my.bed) that looks like:
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*
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* <p/>
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* <pre>
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* <pre>
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* 20 10000000 10000864 CALLABLE
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* 20 10000000 10000864 PASS
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* 20 10000865 10000985 POOR_MAPPING_QUALITY
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* 20 10000865 10000985 POOR_MAPPING_QUALITY
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* 20 10000986 10001138 CALLABLE
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* 20 10000986 10001138 PASS
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* 20 10001139 10001254 POOR_MAPPING_QUALITY
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* 20 10001139 10001254 POOR_MAPPING_QUALITY
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* 20 10001255 10012255 CALLABLE
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* 20 10001255 10012255 PASS
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* 20 10012256 10012259 POOR_MAPPING_QUALITY
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* 20 10012256 10012259 POOR_MAPPING_QUALITY
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* 20 10012260 10012263 CALLABLE
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* 20 10012260 10012263 PASS
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* 20 10012264 10012328 POOR_MAPPING_QUALITY
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* 20 10012264 10012328 POOR_MAPPING_QUALITY
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* 20 10012329 10012550 CALLABLE
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* 20 10012329 10012550 PASS
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* 20 10012551 10012551 LOW_COVERAGE
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* 20 10012551 10012551 LOW_COVERAGE
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* 20 10012552 10012554 CALLABLE
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* 20 10012552 10012554 PASS
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* 20 10012555 10012557 LOW_COVERAGE
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* 20 10012555 10012557 LOW_COVERAGE
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* 20 10012558 10012558 CALLABLE
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* 20 10012558 10012558 PASS
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* et cetera...
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* et cetera...
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* </pre>
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* </pre>
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* as well as a summary table that looks like:
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* as well as a summary table that looks like:
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*
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* <p/>
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* <pre>
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* <pre>
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* state nBases
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* state nBases
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* REF_N 0
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* REF_N 0
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* CALLABLE 996046
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* PASS 996046
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* NO_COVERAGE 121
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* NO_COVERAGE 121
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* LOW_COVERAGE 928
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* LOW_COVERAGE 928
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* EXCESSIVE_COVERAGE 0
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* EXCESSIVE_COVERAGE 0
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@ -139,21 +141,21 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
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byte maxLowMAPQ = 1;
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byte maxLowMAPQ = 1;
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/**
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/**
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* Reads with MAPQ > minMappingQuality are treated as usable for variation detection, contributing to the CALLABLE
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* Reads with MAPQ > minMappingQuality are treated as usable for variation detection, contributing to the PASS
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* state.
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* state.
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*/
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*/
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@Argument(fullName = "minMappingQuality", shortName = "mmq", doc = "Minimum mapping quality of reads to count towards depth.", required = false)
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@Argument(fullName = "minMappingQuality", shortName = "mmq", doc = "Minimum mapping quality of reads to count towards depth.", required = false)
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byte minMappingQuality = 10;
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byte minMappingQuality = 10;
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/**
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/**
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* Bases with less than minBaseQuality are viewed as not sufficiently high quality to contribute to the CALLABLE state
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* Bases with less than minBaseQuality are viewed as not sufficiently high quality to contribute to the PASS state
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*/
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*/
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@Argument(fullName = "minBaseQuality", shortName = "mbq", doc = "Minimum quality of bases to count towards depth.", required = false)
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@Argument(fullName = "minBaseQuality", shortName = "mbq", doc = "Minimum quality of bases to count towards depth.", required = false)
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byte minBaseQuality = 20;
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byte minBaseQuality = 20;
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/**
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/**
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* If the number of QC+ bases (on reads with MAPQ > minMappingQuality and with base quality > minBaseQuality) exceeds this
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* If the number of QC+ bases (on reads with MAPQ > minMappingQuality and with base quality > minBaseQuality) exceeds this
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* value and is less than maxDepth the site is considered CALLABLE.
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* value and is less than maxDepth the site is considered PASS.
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*/
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*/
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@Advanced
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@Advanced
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@Argument(fullName = "minDepth", shortName = "minDepth", doc = "Minimum QC+ read depth before a locus is considered callable", required = false)
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@Argument(fullName = "minDepth", shortName = "minDepth", doc = "Minimum QC+ read depth before a locus is considered callable", required = false)
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@ -191,7 +193,7 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
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public enum OutputFormat {
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public enum OutputFormat {
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/**
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/**
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* The output will be written as a BED file. There's a BED element for each
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* The output will be written as a BED file. There's a BED element for each
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* continuous run of callable states (i.e., CALLABLE, REF_N, etc). This is the recommended
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* continuous run of callable states (i.e., PASS, REF_N, etc). This is the recommended
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* format
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* format
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*/
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*/
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BED,
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BED,
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@ -204,17 +206,29 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
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}
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}
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public enum CalledState {
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public enum CalledState {
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/** the reference base was an N, which is not considered callable the GATK */
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/**
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* the reference base was an N, which is not considered callable the GATK
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*/
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REF_N,
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REF_N,
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/** the base satisfied the min. depth for calling but had less than maxDepth to avoid having EXCESSIVE_COVERAGE */
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/**
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* the base satisfied the min. depth for calling but had less than maxDepth to avoid having EXCESSIVE_COVERAGE
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*/
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CALLABLE,
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CALLABLE,
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/** absolutely no reads were seen at this locus, regardless of the filtering parameters */
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/**
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* absolutely no reads were seen at this locus, regardless of the filtering parameters
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*/
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NO_COVERAGE,
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NO_COVERAGE,
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/** there were less than min. depth bases at the locus, after applying filters */
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/**
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* there were less than min. depth bases at the locus, after applying filters
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*/
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LOW_COVERAGE,
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LOW_COVERAGE,
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/** more than -maxDepth read at the locus, indicating some sort of mapping problem */
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/**
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* more than -maxDepth read at the locus, indicating some sort of mapping problem
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*/
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EXCESSIVE_COVERAGE,
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EXCESSIVE_COVERAGE,
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/** more than --maxFractionOfReadsWithLowMAPQ at the locus, indicating a poor mapping quality of the reads */
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/**
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* more than --maxFractionOfReadsWithLowMAPQ at the locus, indicating a poor mapping quality of the reads
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*/
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POOR_MAPPING_QUALITY
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POOR_MAPPING_QUALITY
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}
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}
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@ -223,11 +237,13 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
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////////////////////////////////////////////////////////////////////////////////////
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////////////////////////////////////////////////////////////////////////////////////
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@Override
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@Override
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public boolean includeReadsWithDeletionAtLoci() { return true; }
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public boolean includeReadsWithDeletionAtLoci() {
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return true;
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}
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@Override
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@Override
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public void initialize() {
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public void initialize() {
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if ( getSampleDB().getSamples().size() != 1 ) {
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if (getSampleDB().getSamples().size() != 1) {
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throw new UserException.BadArgumentValue("-I", "CallableLoci only works for a single sample, but multiple samples were found in the provided BAM files: " + getSampleDB().getSamples());
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throw new UserException.BadArgumentValue("-I", "CallableLoci only works for a single sample, but multiple samples were found in the provided BAM files: " + getSampleDB().getSamples());
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}
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}
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@ -249,7 +265,7 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
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public GenomeLoc loc;
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public GenomeLoc loc;
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final public CalledState state;
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final public CalledState state;
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public CallableBaseState(GenomeLocParser genomeLocParser,GenomeLoc loc, CalledState state) {
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public CallableBaseState(GenomeLocParser genomeLocParser, GenomeLoc loc, CalledState state) {
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this.genomeLocParser = genomeLocParser;
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this.genomeLocParser = genomeLocParser;
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this.loc = loc;
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this.loc = loc;
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this.state = state;
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this.state = state;
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@ -264,12 +280,13 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
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}
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}
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// update routines
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// update routines
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public boolean changingState( CalledState newState ) {
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public boolean changingState(CalledState newState) {
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return state != newState;
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return state != newState;
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}
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}
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/**
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/**
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* Updating the location of this CalledBaseState by the new stop location
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* Updating the location of this CalledBaseState by the new stop location
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*
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* @param newStop
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* @param newStop
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*/
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*/
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public void update(GenomeLoc newStop) {
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public void update(GenomeLoc newStop) {
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@ -285,7 +302,7 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
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public CallableBaseState map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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public CallableBaseState map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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CalledState state;
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CalledState state;
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if ( BaseUtils.isNBase(ref.getBase()) ) {
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if (BaseUtils.isNBase(ref.getBase())) {
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state = CalledState.REF_N;
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state = CalledState.REF_N;
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} else {
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} else {
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// count up the depths of all and QC+ bases
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// count up the depths of all and QC+ bases
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@ -293,29 +310,29 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
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for (PileupElement e : context.getBasePileup()) {
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for (PileupElement e : context.getBasePileup()) {
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rawDepth++;
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rawDepth++;
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if ( e.getMappingQual() <= maxLowMAPQ )
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if (e.getMappingQual() <= maxLowMAPQ)
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lowMAPQDepth++;
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lowMAPQDepth++;
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if ( e.getMappingQual() >= minMappingQuality && ( e.getQual() >= minBaseQuality || e.isDeletion() ) ) {
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if (e.getMappingQual() >= minMappingQuality && (e.getQual() >= minBaseQuality || e.isDeletion())) {
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QCDepth++;
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QCDepth++;
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}
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}
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}
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}
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//System.out.printf("%s rawdepth = %d QCDepth = %d lowMAPQ = %d%n", context.getLocation(), rawDepth, QCDepth, lowMAPQDepth);
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//System.out.printf("%s rawdepth = %d QCDepth = %d lowMAPQ = %d%n", context.getLocation(), rawDepth, QCDepth, lowMAPQDepth);
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if ( rawDepth == 0 ) {
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if (rawDepth == 0) {
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state = CalledState.NO_COVERAGE;
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state = CalledState.NO_COVERAGE;
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} else if ( rawDepth >= minDepthLowMAPQ && MathUtils.ratio( lowMAPQDepth, rawDepth ) >= maxLowMAPQFraction ) {
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} else if (rawDepth >= minDepthLowMAPQ && MathUtils.ratio(lowMAPQDepth, rawDepth) >= maxLowMAPQFraction) {
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state = CalledState.POOR_MAPPING_QUALITY;
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state = CalledState.POOR_MAPPING_QUALITY;
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} else if ( QCDepth < minDepth ) {
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} else if (QCDepth < minDepth) {
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state = CalledState.LOW_COVERAGE;
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state = CalledState.LOW_COVERAGE;
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} else if ( rawDepth >= maxDepth && maxDepth != -1 ) {
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} else if (rawDepth >= maxDepth && maxDepth != -1) {
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state = CalledState.EXCESSIVE_COVERAGE;
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state = CalledState.EXCESSIVE_COVERAGE;
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} else {
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} else {
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state = CalledState.CALLABLE;
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state = CalledState.CALLABLE;
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}
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}
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}
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}
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return new CallableBaseState(getToolkit().getGenomeLocParser(),context.getLocation(), state);
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return new CallableBaseState(getToolkit().getGenomeLocParser(), context.getLocation(), state);
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}
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}
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@Override
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@Override
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@ -328,15 +345,15 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
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// update counts
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// update counts
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integrator.counts[state.getState().ordinal()]++;
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integrator.counts[state.getState().ordinal()]++;
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if ( outputFormat == OutputFormat.STATE_PER_BASE ) {
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if (outputFormat == OutputFormat.STATE_PER_BASE) {
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out.println(state.toString());
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out.println(state.toString());
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}
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}
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// format is integrating
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// format is integrating
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if ( integrator.state == null )
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if (integrator.state == null)
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integrator.state = state;
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integrator.state = state;
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else if ( state.getLocation().getStart() != integrator.state.getLocation().getStop() + 1 ||
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else if (state.getLocation().getStart() != integrator.state.getLocation().getStop() + 1 ||
|
||||||
integrator.state.changingState(state.getState()) ) {
|
integrator.state.changingState(state.getState())) {
|
||||||
out.println(integrator.state.toString());
|
out.println(integrator.state.toString());
|
||||||
integrator.state = state;
|
integrator.state = state;
|
||||||
} else {
|
} else {
|
||||||
|
|
@ -354,14 +371,14 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
|
||||||
@Override
|
@Override
|
||||||
public void onTraversalDone(Integrator result) {
|
public void onTraversalDone(Integrator result) {
|
||||||
// print out the last state
|
// print out the last state
|
||||||
if ( result != null ) {
|
if (result != null) {
|
||||||
if ( outputFormat == OutputFormat.BED ) // get the last interval
|
if (outputFormat == OutputFormat.BED) // get the last interval
|
||||||
out.println(result.state.toString());
|
out.println(result.state.toString());
|
||||||
|
|
||||||
try {
|
try {
|
||||||
PrintStream summaryOut = new PrintStream(summaryFile);
|
PrintStream summaryOut = new PrintStream(summaryFile);
|
||||||
summaryOut.printf("%30s %s%n", "state", "nBases");
|
summaryOut.printf("%30s %s%n", "state", "nBases");
|
||||||
for ( CalledState state : CalledState.values() ) {
|
for (CalledState state : CalledState.values()) {
|
||||||
summaryOut.printf("%30s %d%n", state, result.counts[state.ordinal()]);
|
summaryOut.printf("%30s %d%n", state, result.counts[state.ordinal()]);
|
||||||
}
|
}
|
||||||
summaryOut.close();
|
summaryOut.close();
|
||||||
|
|
|
||||||
|
|
@ -1,3 +1,27 @@
|
||||||
|
/*
|
||||||
|
* Copyright (c) 2012, The Broad Institute
|
||||||
|
*
|
||||||
|
* Permission is hereby granted, free of charge, to any person
|
||||||
|
* obtaining a copy of this software and associated documentation
|
||||||
|
* files (the "Software"), to deal in the Software without
|
||||||
|
* restriction, including without limitation the rights to use,
|
||||||
|
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||||
|
* copies of the Software, and to permit persons to whom the
|
||||||
|
* Software is furnished to do so, subject to the following
|
||||||
|
* conditions:
|
||||||
|
*
|
||||||
|
* The above copyright notice and this permission notice shall be
|
||||||
|
* included in all copies or substantial portions of the Software.
|
||||||
|
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||||
|
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||||
|
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||||
|
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||||
|
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||||
|
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||||
|
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
||||||
|
* OTHER DEALINGS IN THE SOFTWARE.
|
||||||
|
*/
|
||||||
|
|
||||||
package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
|
package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
|
||||||
|
|
||||||
/**
|
/**
|
||||||
|
|
@ -7,16 +31,40 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
|
||||||
* @since 2/1/12
|
* @since 2/1/12
|
||||||
*/
|
*/
|
||||||
public enum CallableStatus {
|
public enum CallableStatus {
|
||||||
/** the reference base was an N, which is not considered callable the GATK */
|
/**
|
||||||
REF_N,
|
* the reference base was an N, which is not considered callable the GATK
|
||||||
/** the base satisfied the min. depth for calling but had less than maxDepth to avoid having EXCESSIVE_COVERAGE */
|
*/
|
||||||
CALLABLE,
|
// todo -- implement this status
|
||||||
/** absolutely no reads were seen at this locus, regardless of the filtering parameters */
|
REF_N("the reference base was an N, which is not considered callable the GATK"),
|
||||||
NO_COVERAGE,
|
/**
|
||||||
/** there were less than min. depth bases at the locus, after applying filters */
|
* the base satisfied the min. depth for calling but had less than maxDepth to avoid having EXCESSIVE_COVERAGE
|
||||||
LOW_COVERAGE,
|
*/
|
||||||
/** more than -maxDepth read at the locus, indicating some sort of mapping problem */
|
PASS("the base satisfied the min. depth for calling but had less than maxDepth to avoid having EXCESSIVE_COVERAGE"),
|
||||||
EXCESSIVE_COVERAGE,
|
/**
|
||||||
/** more than --maxFractionOfReadsWithLowMAPQ at the locus, indicating a poor mapping quality of the reads */
|
* absolutely no reads were seen at this locus, regardless of the filtering parameters
|
||||||
POOR_QUALITY
|
*/
|
||||||
|
NO_COVERAGE("absolutely no reads were seen at this locus, regardless of the filtering parameters"),
|
||||||
|
/**
|
||||||
|
* there were less than min. depth bases at the locus, after applying filters
|
||||||
|
*/
|
||||||
|
LOW_COVERAGE("there were less than min. depth bases at the locus, after applying filters"),
|
||||||
|
/**
|
||||||
|
* more than -maxDepth read at the locus, indicating some sort of mapping problem
|
||||||
|
*/
|
||||||
|
EXCESSIVE_COVERAGE("more than -maxDepth read at the locus, indicating some sort of mapping problem"),
|
||||||
|
/**
|
||||||
|
* more than --maxFractionOfReadsWithLowMAPQ at the locus, indicating a poor mapping quality of the reads
|
||||||
|
*/
|
||||||
|
POOR_QUALITY("more than --maxFractionOfReadsWithLowMAPQ at the locus, indicating a poor mapping quality of the reads"),
|
||||||
|
|
||||||
|
BAD_MATE(""),
|
||||||
|
|
||||||
|
INCONSISTENT_COVERAGE("");
|
||||||
|
|
||||||
|
|
||||||
|
public String description;
|
||||||
|
|
||||||
|
private CallableStatus(String description) {
|
||||||
|
this.description = description;
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -1,45 +1,67 @@
|
||||||
|
/*
|
||||||
|
* Copyright (c) 2012, The Broad Institute
|
||||||
|
*
|
||||||
|
* Permission is hereby granted, free of charge, to any person
|
||||||
|
* obtaining a copy of this software and associated documentation
|
||||||
|
* files (the "Software"), to deal in the Software without
|
||||||
|
* restriction, including without limitation the rights to use,
|
||||||
|
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||||
|
* copies of the Software, and to permit persons to whom the
|
||||||
|
* Software is furnished to do so, subject to the following
|
||||||
|
* conditions:
|
||||||
|
*
|
||||||
|
* The above copyright notice and this permission notice shall be
|
||||||
|
* included in all copies or substantial portions of the Software.
|
||||||
|
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||||
|
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||||
|
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||||
|
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||||
|
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||||
|
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||||
|
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
||||||
|
* OTHER DEALINGS IN THE SOFTWARE.
|
||||||
|
*/
|
||||||
|
|
||||||
package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
|
package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
|
||||||
|
|
||||||
import org.broad.tribble.Feature;
|
import org.broad.tribble.Feature;
|
||||||
import org.broadinstitute.sting.commandline.Argument;
|
import org.broadinstitute.sting.commandline.*;
|
||||||
import org.broadinstitute.sting.commandline.Input;
|
|
||||||
import org.broadinstitute.sting.commandline.IntervalBinding;
|
|
||||||
import org.broadinstitute.sting.commandline.Output;
|
|
||||||
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
||||||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||||
import org.broadinstitute.sting.gatk.walkers.By;
|
import org.broadinstitute.sting.gatk.walkers.*;
|
||||||
import org.broadinstitute.sting.gatk.walkers.DataSource;
|
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
|
||||||
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
|
|
||||||
import org.broadinstitute.sting.utils.GenomeLoc;
|
import org.broadinstitute.sting.utils.GenomeLoc;
|
||||||
import org.broadinstitute.sting.utils.GenomeLocComparator;
|
import org.broadinstitute.sting.utils.GenomeLocComparator;
|
||||||
import org.broadinstitute.sting.utils.GenomeLocParser;
|
import org.broadinstitute.sting.utils.GenomeLocParser;
|
||||||
|
import org.broadinstitute.sting.utils.SampleUtils;
|
||||||
|
import org.broadinstitute.sting.utils.codecs.vcf.*;
|
||||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||||
|
import org.broadinstitute.sting.utils.variantcontext.Allele;
|
||||||
|
import org.broadinstitute.sting.utils.variantcontext.Genotype;
|
||||||
|
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||||
|
import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
|
||||||
|
|
||||||
import java.io.PrintStream;
|
import java.util.*;
|
||||||
import java.util.HashMap;
|
|
||||||
import java.util.Iterator;
|
|
||||||
import java.util.List;
|
|
||||||
import java.util.TreeSet;
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* Short one line description of the walker.
|
* Short one line description of the walker.
|
||||||
*
|
* <p/>
|
||||||
* <p>
|
* <p>
|
||||||
* [Long description of the walker]
|
* [Long description of the walker]
|
||||||
* </p>
|
* </p>
|
||||||
*
|
* <p/>
|
||||||
*
|
* <p/>
|
||||||
* <h2>Input</h2>
|
* <h2>Input</h2>
|
||||||
* <p>
|
* <p>
|
||||||
* [Description of the Input]
|
* [Description of the Input]
|
||||||
* </p>
|
* </p>
|
||||||
*
|
* <p/>
|
||||||
* <h2>Output</h2>
|
* <h2>Output</h2>
|
||||||
* <p>
|
* <p>
|
||||||
* [Description of the Output]
|
* [Description of the Output]
|
||||||
* </p>
|
* </p>
|
||||||
*
|
* <p/>
|
||||||
* <h2>Examples</h2>
|
* <h2>Examples</h2>
|
||||||
* <pre>
|
* <pre>
|
||||||
* java
|
* java
|
||||||
|
|
@ -51,12 +73,13 @@ import java.util.TreeSet;
|
||||||
* @since 2/1/12
|
* @since 2/1/12
|
||||||
*/
|
*/
|
||||||
@By(value = DataSource.READS)
|
@By(value = DataSource.READS)
|
||||||
public class DiagnoseTargets extends LocusWalker<Long, Long> {
|
@PartitionBy(PartitionType.INTERVAL)
|
||||||
|
public class DiagnoseTargets extends LocusWalker<Long, Long> implements AnnotatorCompatibleWalker {
|
||||||
@Input(fullName = "interval_track", shortName = "int", doc = "", required = true)
|
@Input(fullName = "interval_track", shortName = "int", doc = "", required = true)
|
||||||
private IntervalBinding<Feature> intervalTrack = null;
|
private IntervalBinding<Feature> intervalTrack = null;
|
||||||
|
|
||||||
@Output
|
@Output(doc = "File to which variants should be written", required = true)
|
||||||
private PrintStream out = System.out;
|
protected VCFWriter vcfWriter = null;
|
||||||
|
|
||||||
@Argument(fullName = "expand_interval", shortName = "exp", doc = "", required = false)
|
@Argument(fullName = "expand_interval", shortName = "exp", doc = "", required = false)
|
||||||
private int expandInterval = 50;
|
private int expandInterval = 50;
|
||||||
|
|
@ -73,13 +96,13 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
|
||||||
@Argument(fullName = "maximum_coverage", shortName = "maxcov", doc = "", required = false)
|
@Argument(fullName = "maximum_coverage", shortName = "maxcov", doc = "", required = false)
|
||||||
private int maximumCoverage = 700;
|
private int maximumCoverage = 700;
|
||||||
|
|
||||||
private TreeSet<GenomeLoc> intervalList = null; // The list of intervals of interest (plus expanded intervals if user wants them)
|
private TreeSet<GenomeLoc> intervalList = null; // The list of intervals of interest (plus expanded intervals if user wants them)
|
||||||
private HashMap<GenomeLoc, IntervalStatistics> intervalMap = null; // interval => statistics
|
private HashMap<GenomeLoc, IntervalStatistics> intervalMap = null; // interval => statistics
|
||||||
private Iterator<GenomeLoc> intervalListIterator; // An iterator to go over all the intervals provided as we traverse the genome
|
private Iterator<GenomeLoc> intervalListIterator; // An iterator to go over all the intervals provided as we traverse the genome
|
||||||
private GenomeLoc currentInterval = null; // The "current" interval loaded and being filled with statistics
|
private GenomeLoc currentInterval = null; // The "current" interval loaded
|
||||||
private IntervalStatistics currentIntervalStatistics = null; // The "current" interval loaded and being filled with statistics
|
private IntervalStatistics currentIntervalStatistics = null; // The "current" interval being filled with statistics
|
||||||
|
private Set<String> samples = null; // All the samples being processed
|
||||||
private GenomeLocParser parser; // just an object to allow us to create genome locs (for the expanded intervals)
|
private GenomeLocParser parser; // just an object to allow us to create genome locs (for the expanded intervals)
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
public void initialize() {
|
public void initialize() {
|
||||||
|
|
@ -88,38 +111,72 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
|
||||||
if (intervalTrack == null)
|
if (intervalTrack == null)
|
||||||
throw new UserException("This tool currently only works if you provide an interval track");
|
throw new UserException("This tool currently only works if you provide an interval track");
|
||||||
|
|
||||||
parser = new GenomeLocParser(getToolkit().getMasterSequenceDictionary()); // Important to initialize the parser before creating the intervals below
|
parser = new GenomeLocParser(getToolkit().getMasterSequenceDictionary()); // Important to initialize the parser before creating the intervals below
|
||||||
|
|
||||||
List<GenomeLoc> originalList = intervalTrack.getIntervals(getToolkit()); // The original list of targets provided by the user that will be expanded or not depending on the options provided
|
List<GenomeLoc> originalList = intervalTrack.getIntervals(getToolkit()); // The original list of targets provided by the user that will be expanded or not depending on the options provided
|
||||||
intervalList = new TreeSet<GenomeLoc>(new GenomeLocComparator());
|
intervalList = new TreeSet<GenomeLoc>(new GenomeLocComparator());
|
||||||
intervalMap = new HashMap<GenomeLoc, IntervalStatistics>(originalList.size() * 2);
|
intervalMap = new HashMap<GenomeLoc, IntervalStatistics>();
|
||||||
for (GenomeLoc interval : originalList)
|
for (GenomeLoc interval : originalList)
|
||||||
addAndExpandIntervalToLists(interval);
|
intervalList.add(interval);
|
||||||
|
//addAndExpandIntervalToMap(interval);
|
||||||
|
|
||||||
intervalListIterator = intervalList.iterator();
|
intervalListIterator = intervalList.iterator();
|
||||||
|
|
||||||
|
// get all of the unique sample names
|
||||||
|
samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
|
||||||
|
|
||||||
|
// initialize the header
|
||||||
|
Set<VCFHeaderLine> headerInfo = getHeaderInfo();
|
||||||
|
|
||||||
|
vcfWriter.writeHeader(new VCFHeader(headerInfo, samples));
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Gets the header lines for the VCF writer
|
||||||
|
*
|
||||||
|
* @return A set of VCF header lines
|
||||||
|
*/
|
||||||
|
private Set<VCFHeaderLine> getHeaderInfo() {
|
||||||
|
Set<VCFHeaderLine> headerLines = new HashSet<VCFHeaderLine>();
|
||||||
|
|
||||||
|
// INFO fields for overall data
|
||||||
|
headerLines.add(new VCFInfoHeaderLine("END", 1, VCFHeaderLineType.Integer, "Stop position of the interval"));
|
||||||
|
headerLines.add(new VCFInfoHeaderLine("DP", 1, VCFHeaderLineType.Integer, "Total depth in the site. Sum of the depth of all pools"));
|
||||||
|
headerLines.add(new VCFInfoHeaderLine("AD", 1, VCFHeaderLineType.Float, "Average depth across the interval. Sum of the depth in a lci divided by interval size."));
|
||||||
|
headerLines.add(new VCFInfoHeaderLine("Diagnose Targets", 0, VCFHeaderLineType.Flag, "DiagnoseTargets mode"));
|
||||||
|
|
||||||
|
// FORMAT fields for each genotype
|
||||||
|
headerLines.add(new VCFFormatHeaderLine("DP", 1, VCFHeaderLineType.Integer, "Total depth in the site. Sum of the depth of all pools"));
|
||||||
|
headerLines.add(new VCFFormatHeaderLine("AD", 1, VCFHeaderLineType.Float, "Average depth across the interval. Sum of the depth in a lci divided by interval size."));
|
||||||
|
|
||||||
|
// FILTER fields
|
||||||
|
|
||||||
|
for (CallableStatus stat : CallableStatus.values()) {
|
||||||
|
headerLines.add(new VCFHeaderLine(stat.name(), stat.description));
|
||||||
|
}
|
||||||
|
|
||||||
|
return headerLines;
|
||||||
}
|
}
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
public Long map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
|
public Long map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
|
||||||
GenomeLoc refLocus = ref.getLocus();
|
GenomeLoc refLocus = ref.getLocus();
|
||||||
while (currentInterval == null || currentInterval.isBefore(refLocus)) {
|
while (currentInterval == null || currentInterval.isBefore(refLocus)) { // do this for first time and while currentInterval is behind current locus
|
||||||
if (!intervalListIterator.hasNext())
|
if (!intervalListIterator.hasNext())
|
||||||
return 0L;
|
return 0L;
|
||||||
|
|
||||||
|
if (currentInterval != null)
|
||||||
|
processIntervalStats(currentInterval, Allele.create(ref.getBase(), true));
|
||||||
|
|
||||||
currentInterval = intervalListIterator.next();
|
currentInterval = intervalListIterator.next();
|
||||||
|
addAndExpandIntervalToMap(currentInterval);
|
||||||
currentIntervalStatistics = intervalMap.get(currentInterval);
|
currentIntervalStatistics = intervalMap.get(currentInterval);
|
||||||
}
|
}
|
||||||
|
|
||||||
if (currentInterval.isPast(refLocus))
|
if (currentInterval.isPast(refLocus)) // skip if we are behind the current interval
|
||||||
return 0L;
|
return 0L;
|
||||||
|
|
||||||
byte[] mappingQualities = context.getBasePileup().getMappingQuals();
|
currentIntervalStatistics.addLocus(context); // Add current locus to stats
|
||||||
byte[] baseQualities = context.getBasePileup().getQuals();
|
|
||||||
int coverage = context.getBasePileup().getBaseAndMappingFilteredPileup(minimumBaseQuality, minimumMappingQuality).depthOfCoverage();
|
|
||||||
int rawCoverage = context.size();
|
|
||||||
|
|
||||||
IntervalStatisticLocus locusData = new IntervalStatisticLocus(mappingQualities, baseQualities, coverage, rawCoverage);
|
|
||||||
currentIntervalStatistics.addLocus(refLocus, locusData);
|
|
||||||
|
|
||||||
return 1L;
|
return 1L;
|
||||||
}
|
}
|
||||||
|
|
@ -129,6 +186,13 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
|
||||||
return 0L;
|
return 0L;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Not sure what we are going to do here
|
||||||
|
*
|
||||||
|
* @param value result of the map.
|
||||||
|
* @param sum accumulator for the reduce.
|
||||||
|
* @return a long
|
||||||
|
*/
|
||||||
@Override
|
@Override
|
||||||
public Long reduce(Long value, Long sum) {
|
public Long reduce(Long value, Long sum) {
|
||||||
return sum + value;
|
return sum + value;
|
||||||
|
|
@ -136,14 +200,25 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
public void onTraversalDone(Long result) {
|
public void onTraversalDone(Long result) {
|
||||||
super.onTraversalDone(result);
|
for (GenomeLoc interval : intervalMap.keySet())
|
||||||
out.println("Interval\tCallStatus\tCOV\tAVG");
|
processIntervalStats(interval, Allele.create("<DT>", true));
|
||||||
for (GenomeLoc interval : intervalList) {
|
|
||||||
IntervalStatistics stats = intervalMap.get(interval);
|
|
||||||
out.println(String.format("%s\t%s\t%d\t%f", interval, stats.callableStatus(), stats.totalCoverage(), stats.averageCoverage()));
|
|
||||||
}
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public RodBinding<VariantContext> getSnpEffRodBinding() {return null;}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public RodBinding<VariantContext> getDbsnpRodBinding() {return null;}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public List<RodBinding<VariantContext>> getCompRodBindings() {return null;}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public List<RodBinding<VariantContext>> getResourceRodBindings() {return null;}
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public boolean alwaysAppendDbsnpId() {return false;}
|
||||||
|
|
||||||
private GenomeLoc createIntervalBefore(GenomeLoc interval) {
|
private GenomeLoc createIntervalBefore(GenomeLoc interval) {
|
||||||
int start = Math.max(interval.getStart() - expandInterval, 0);
|
int start = Math.max(interval.getStart() - expandInterval, 0);
|
||||||
int stop = Math.max(interval.getStart() - 1, 0);
|
int stop = Math.max(interval.getStart() - 1, 0);
|
||||||
|
|
@ -157,16 +232,75 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
|
||||||
return parser.createGenomeLoc(interval.getContig(), interval.getContigIndex(), start, stop);
|
return parser.createGenomeLoc(interval.getContig(), interval.getContigIndex(), start, stop);
|
||||||
}
|
}
|
||||||
|
|
||||||
private void addAndExpandIntervalToLists(GenomeLoc interval) {
|
/**
|
||||||
|
* Takes an interval and commits it to memory.
|
||||||
|
* It will expand it if so told by the -exp command line argument
|
||||||
|
*
|
||||||
|
* @param interval The new interval to process
|
||||||
|
*/
|
||||||
|
private void addAndExpandIntervalToMap(GenomeLoc interval) {
|
||||||
if (expandInterval > 0) {
|
if (expandInterval > 0) {
|
||||||
GenomeLoc before = createIntervalBefore(interval);
|
GenomeLoc before = createIntervalBefore(interval);
|
||||||
GenomeLoc after = createIntervalAfter(interval);
|
GenomeLoc after = createIntervalAfter(interval);
|
||||||
intervalList.add(before);
|
intervalList.add(before);
|
||||||
intervalList.add(after);
|
intervalList.add(after);
|
||||||
intervalMap.put(before, new IntervalStatistics(before, minimumCoverage, maximumCoverage, minimumMappingQuality, minimumBaseQuality));
|
intervalMap.put(before, new IntervalStatistics(samples, before, minimumCoverage, maximumCoverage, minimumMappingQuality, minimumBaseQuality));
|
||||||
intervalMap.put(after, new IntervalStatistics(after, minimumCoverage, maximumCoverage, minimumMappingQuality, minimumBaseQuality));
|
intervalMap.put(after, new IntervalStatistics(samples, after, minimumCoverage, maximumCoverage, minimumMappingQuality, minimumBaseQuality));
|
||||||
}
|
}
|
||||||
intervalList.add(interval);
|
if (!intervalList.contains(interval))
|
||||||
intervalMap.put(interval, new IntervalStatistics(interval, minimumCoverage, maximumCoverage, minimumMappingQuality, minimumBaseQuality));
|
intervalList.add(interval);
|
||||||
|
intervalMap.put(interval, new IntervalStatistics(samples, interval, minimumCoverage, maximumCoverage, minimumMappingQuality, minimumBaseQuality));
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Takes the interval, finds it in the stash, prints it to the VCF, and removes it
|
||||||
|
*
|
||||||
|
* @param interval The interval in memory that you want to write out and clear
|
||||||
|
* @param allele the allele
|
||||||
|
*/
|
||||||
|
private void processIntervalStats(GenomeLoc interval, Allele allele) {
|
||||||
|
IntervalStatistics stats = intervalMap.get(interval);
|
||||||
|
|
||||||
|
List<Allele> alleles = new ArrayList<Allele>();
|
||||||
|
Map<String, Object> attributes = new HashMap<String, Object>();
|
||||||
|
ArrayList<Genotype> genotypes = new ArrayList<Genotype>();
|
||||||
|
|
||||||
|
alleles.add(allele);
|
||||||
|
VariantContextBuilder vcb = new VariantContextBuilder("DiagnoseTargets", interval.getContig(), interval.getStart(), interval.getStop(), alleles);
|
||||||
|
|
||||||
|
vcb = vcb.log10PError(VariantContext.NO_LOG10_PERROR); // QUAL field makes no sense in our VCF
|
||||||
|
vcb.filters(statusesToStrings(stats.callableStatuses()));
|
||||||
|
|
||||||
|
attributes.put(VCFConstants.END_KEY, interval.getStop());
|
||||||
|
attributes.put(VCFConstants.DEPTH_KEY, stats.totalCoverage());
|
||||||
|
attributes.put("AV", stats.averageCoverage());
|
||||||
|
|
||||||
|
vcb = vcb.attributes(attributes);
|
||||||
|
|
||||||
|
for (String sample : samples) {
|
||||||
|
Map<String, Object> infos = new HashMap<String, Object>();
|
||||||
|
infos.put("DP", stats.getSample(sample).totalCoverage());
|
||||||
|
infos.put("AV", stats.getSample(sample).averageCoverage());
|
||||||
|
|
||||||
|
Set<String> filters = new HashSet<String>();
|
||||||
|
filters.addAll(statusesToStrings(stats.getSample(sample).getCallableStatuses()));
|
||||||
|
|
||||||
|
|
||||||
|
genotypes.add(new Genotype(sample, alleles, VariantContext.NO_LOG10_PERROR, filters, infos, false));
|
||||||
|
}
|
||||||
|
vcb = vcb.genotypes(genotypes);
|
||||||
|
|
||||||
|
vcfWriter.add(vcb.make());
|
||||||
|
|
||||||
|
intervalMap.remove(interval);
|
||||||
|
}
|
||||||
|
|
||||||
|
private static Set<String> statusesToStrings(Set<CallableStatus> statuses) {
|
||||||
|
Set<String> output = new HashSet<String>(statuses.size());
|
||||||
|
|
||||||
|
for (CallableStatus status : statuses)
|
||||||
|
output.add(status.name());
|
||||||
|
|
||||||
|
return output;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -1,34 +0,0 @@
|
||||||
package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
|
|
||||||
|
|
||||||
/**
|
|
||||||
* The definition of a locus for the DiagnoseTargets walker statistics calculation
|
|
||||||
*
|
|
||||||
* @author Mauricio Carneiro
|
|
||||||
* @since 2/3/12
|
|
||||||
*/
|
|
||||||
class IntervalStatisticLocus {
|
|
||||||
private final byte[] mappingQuality;
|
|
||||||
private final byte[] baseQuality;
|
|
||||||
private final int coverage;
|
|
||||||
private final int rawCoverage;
|
|
||||||
|
|
||||||
public IntervalStatisticLocus(byte[] mappingQuality, byte[] baseQuality, int coverage, int rawCoverage) {
|
|
||||||
this.mappingQuality = mappingQuality;
|
|
||||||
this.baseQuality = baseQuality;
|
|
||||||
this.coverage = coverage;
|
|
||||||
this.rawCoverage = rawCoverage;
|
|
||||||
}
|
|
||||||
|
|
||||||
public IntervalStatisticLocus() {
|
|
||||||
this(new byte[1], new byte[1], 0, 0);
|
|
||||||
}
|
|
||||||
|
|
||||||
public int getCoverage() {
|
|
||||||
return coverage;
|
|
||||||
}
|
|
||||||
|
|
||||||
public int getRawCoverage() {
|
|
||||||
return rawCoverage;
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
@ -1,44 +1,62 @@
|
||||||
|
/*
|
||||||
|
* Copyright (c) 2012, The Broad Institute
|
||||||
|
*
|
||||||
|
* Permission is hereby granted, free of charge, to any person
|
||||||
|
* obtaining a copy of this software and associated documentation
|
||||||
|
* files (the "Software"), to deal in the Software without
|
||||||
|
* restriction, including without limitation the rights to use,
|
||||||
|
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||||
|
* copies of the Software, and to permit persons to whom the
|
||||||
|
* Software is furnished to do so, subject to the following
|
||||||
|
* conditions:
|
||||||
|
*
|
||||||
|
* The above copyright notice and this permission notice shall be
|
||||||
|
* included in all copies or substantial portions of the Software.
|
||||||
|
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||||
|
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||||
|
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||||
|
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||||
|
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||||
|
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||||
|
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
||||||
|
* OTHER DEALINGS IN THE SOFTWARE.
|
||||||
|
*/
|
||||||
|
|
||||||
package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
|
package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
|
||||||
|
|
||||||
|
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
||||||
import org.broadinstitute.sting.utils.GenomeLoc;
|
import org.broadinstitute.sting.utils.GenomeLoc;
|
||||||
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
|
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
|
||||||
|
|
||||||
import java.util.ArrayList;
|
|
||||||
import java.util.HashMap;
|
import java.util.HashMap;
|
||||||
|
import java.util.HashSet;
|
||||||
|
import java.util.Map;
|
||||||
|
import java.util.Set;
|
||||||
|
|
||||||
/**
|
public class IntervalStatistics {
|
||||||
* Short one line description of the walker.
|
|
||||||
*
|
private final Map<String, SampleStatistics> samples;
|
||||||
* @author Mauricio Carneiro
|
|
||||||
* @since 2/1/12
|
|
||||||
*/
|
|
||||||
class IntervalStatistics {
|
|
||||||
private final GenomeLoc interval;
|
private final GenomeLoc interval;
|
||||||
private final ArrayList<IntervalStatisticLocus> loci;
|
|
||||||
|
|
||||||
private final int minimumCoverageThreshold;
|
private int preComputedTotalCoverage = -1; // avoids re-calculating the total sum (-1 means we haven't pre-computed it yet)
|
||||||
private final int maximumCoverageThreshold;
|
|
||||||
private final int minimumMappingQuality;
|
|
||||||
private final int minimumBaseQuality;
|
|
||||||
|
|
||||||
private int preComputedTotalCoverage = -1; // avoids re-calculating the total sum (-1 means we haven't pre-computed it yet)
|
|
||||||
|
|
||||||
private IntervalStatistics(GenomeLoc interval, ArrayList<IntervalStatisticLocus> loci, int minimumCoverageThreshold, int maximumCoverageThreshold, int minimumMappingQuality, int minimumBaseQuality) {
|
public IntervalStatistics(Set<String> samples, GenomeLoc interval, int minimumCoverageThreshold, int maximumCoverageThreshold, int minimumMappingQuality, int minimumBaseQuality) {
|
||||||
this.interval = interval;
|
this.interval = interval;
|
||||||
this.loci = loci;
|
this.samples = new HashMap<String, SampleStatistics>(samples.size());
|
||||||
this.minimumCoverageThreshold = minimumCoverageThreshold;
|
for (String sample : samples)
|
||||||
this.maximumCoverageThreshold = maximumCoverageThreshold;
|
this.samples.put(sample, new SampleStatistics(interval, minimumCoverageThreshold, maximumCoverageThreshold, minimumMappingQuality, minimumBaseQuality));
|
||||||
this.minimumMappingQuality = minimumMappingQuality;
|
|
||||||
this.minimumBaseQuality = minimumBaseQuality;
|
|
||||||
}
|
}
|
||||||
|
|
||||||
public IntervalStatistics(GenomeLoc interval, int minimumCoverageThreshold, int maximumCoverageThreshold, int minimumMappingQuality, int minimumBaseQuality) {
|
public SampleStatistics getSample(String sample) {
|
||||||
this(interval, new ArrayList<IntervalStatisticLocus>(interval.size()), minimumCoverageThreshold, maximumCoverageThreshold, minimumMappingQuality, minimumBaseQuality);
|
return samples.get(sample);
|
||||||
|
}
|
||||||
|
|
||||||
// Initialize every loci (this way we don't have to worry about non-existent loci in the object
|
public void addLocus(AlignmentContext context) {
|
||||||
for (int i = 0; i < interval.size(); i++)
|
ReadBackedPileup pileup = context.getBasePileup();
|
||||||
this.loci.add(i, new IntervalStatisticLocus());
|
|
||||||
|
|
||||||
|
for (String sample : samples.keySet())
|
||||||
|
getSample(sample).addLocus(context.getLocation(), pileup.getPileupForSample(sample));
|
||||||
}
|
}
|
||||||
|
|
||||||
public long totalCoverage() {
|
public long totalCoverage() {
|
||||||
|
|
@ -50,73 +68,27 @@ class IntervalStatistics {
|
||||||
public double averageCoverage() {
|
public double averageCoverage() {
|
||||||
if (preComputedTotalCoverage < 0)
|
if (preComputedTotalCoverage < 0)
|
||||||
calculateTotalCoverage();
|
calculateTotalCoverage();
|
||||||
return (double) preComputedTotalCoverage / loci.size();
|
return (double) preComputedTotalCoverage / interval.size();
|
||||||
}
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Calculates the callable status of the entire interval
|
|
||||||
*
|
|
||||||
* @return the callable status of the entire interval
|
|
||||||
*/
|
|
||||||
public CallableStatus callableStatus() {
|
|
||||||
long max = -1;
|
|
||||||
CallableStatus maxCallableStatus = null;
|
|
||||||
HashMap<CallableStatus, Integer> statusCounts = new HashMap<CallableStatus, Integer>(CallableStatus.values().length);
|
|
||||||
|
|
||||||
// initialize the statusCounts with all callable states
|
|
||||||
for (CallableStatus key : CallableStatus.values())
|
|
||||||
statusCounts.put(key, 0);
|
|
||||||
|
|
||||||
// calculate the callable status for each locus
|
|
||||||
for (int i = 0; i < loci.size(); i++) {
|
|
||||||
CallableStatus status = callableStatus(i);
|
|
||||||
int count = statusCounts.get(status) + 1;
|
|
||||||
statusCounts.put(status, count);
|
|
||||||
|
|
||||||
if (count > max) {
|
|
||||||
max = count;
|
|
||||||
maxCallableStatus = status;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
return maxCallableStatus;
|
|
||||||
}
|
|
||||||
|
|
||||||
public void addLocus(GenomeLoc locus, IntervalStatisticLocus locusData) {
|
|
||||||
if (!interval.containsP(locus))
|
|
||||||
throw new ReviewedStingException(String.format("Locus %s is not part of the Interval", locus));
|
|
||||||
|
|
||||||
int locusIndex = locus.getStart() - interval.getStart();
|
|
||||||
|
|
||||||
loci.add(locusIndex, locusData);
|
|
||||||
}
|
|
||||||
|
|
||||||
/**
|
|
||||||
* returns the callable status of this locus without taking the reference base into account.
|
|
||||||
*
|
|
||||||
* @param locusIndex location in the genome to inquire (only one locus)
|
|
||||||
* @return the callable status of a locus
|
|
||||||
*/
|
|
||||||
private CallableStatus callableStatus(int locusIndex) {
|
|
||||||
if (loci.get(locusIndex).getCoverage() > maximumCoverageThreshold)
|
|
||||||
return CallableStatus.EXCESSIVE_COVERAGE;
|
|
||||||
|
|
||||||
if (loci.get(locusIndex).getCoverage() >= minimumCoverageThreshold)
|
|
||||||
return CallableStatus.CALLABLE;
|
|
||||||
|
|
||||||
if (loci.get(locusIndex).getRawCoverage() >= minimumCoverageThreshold)
|
|
||||||
return CallableStatus.POOR_QUALITY;
|
|
||||||
|
|
||||||
if (loci.get(locusIndex).getRawCoverage() > 0)
|
|
||||||
return CallableStatus.LOW_COVERAGE;
|
|
||||||
|
|
||||||
return CallableStatus.NO_COVERAGE;
|
|
||||||
}
|
}
|
||||||
|
|
||||||
private void calculateTotalCoverage() {
|
private void calculateTotalCoverage() {
|
||||||
preComputedTotalCoverage = 0;
|
preComputedTotalCoverage = 0;
|
||||||
for (IntervalStatisticLocus locus : loci)
|
for (SampleStatistics sample : samples.values())
|
||||||
preComputedTotalCoverage += locus.getCoverage();
|
preComputedTotalCoverage += sample.totalCoverage();
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Return the Callable statuses for the interval as a whole
|
||||||
|
* todo -- add a voting system for sample flags and add interval specific statuses
|
||||||
|
*
|
||||||
|
* @return the callable status(es) for the whole interval
|
||||||
|
*/
|
||||||
|
public Set<CallableStatus> callableStatuses() {
|
||||||
|
Set<CallableStatus> output = new HashSet<CallableStatus>();
|
||||||
|
|
||||||
|
for (SampleStatistics sample : samples.values())
|
||||||
|
output.addAll(sample.getCallableStatuses());
|
||||||
|
|
||||||
|
return output;
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,83 @@
|
||||||
|
/*
|
||||||
|
* Copyright (c) 2012, The Broad Institute
|
||||||
|
*
|
||||||
|
* Permission is hereby granted, free of charge, to any person
|
||||||
|
* obtaining a copy of this software and associated documentation
|
||||||
|
* files (the "Software"), to deal in the Software without
|
||||||
|
* restriction, including without limitation the rights to use,
|
||||||
|
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||||
|
* copies of the Software, and to permit persons to whom the
|
||||||
|
* Software is furnished to do so, subject to the following
|
||||||
|
* conditions:
|
||||||
|
*
|
||||||
|
* The above copyright notice and this permission notice shall be
|
||||||
|
* included in all copies or substantial portions of the Software.
|
||||||
|
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||||
|
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||||
|
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||||
|
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||||
|
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||||
|
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||||
|
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
||||||
|
* OTHER DEALINGS IN THE SOFTWARE.
|
||||||
|
*/
|
||||||
|
|
||||||
|
package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
|
||||||
|
|
||||||
|
import java.util.HashSet;
|
||||||
|
import java.util.Set;
|
||||||
|
|
||||||
|
public class LocusStatistics {
|
||||||
|
final int coverage;
|
||||||
|
final int rawCoverage;
|
||||||
|
|
||||||
|
public LocusStatistics() {
|
||||||
|
this.coverage = 0;
|
||||||
|
this.rawCoverage = 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
public LocusStatistics(int coverage, int rawCoverage) {
|
||||||
|
this.coverage = coverage;
|
||||||
|
this.rawCoverage = rawCoverage;
|
||||||
|
}
|
||||||
|
|
||||||
|
public int getCoverage() {
|
||||||
|
return coverage;
|
||||||
|
}
|
||||||
|
|
||||||
|
public int getRawCoverage() {
|
||||||
|
return rawCoverage;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Generates all applicable statuses from the coverages in this locus
|
||||||
|
*
|
||||||
|
* @param minimumCoverageThreshold the minimum threshold for determining low coverage/poor quality
|
||||||
|
* @param maximumCoverageThreshold the maximum threshold for determining excessive coverage
|
||||||
|
* @return a set of all statuses that apply
|
||||||
|
*/
|
||||||
|
public Set<CallableStatus> callableStatuses(int minimumCoverageThreshold, int maximumCoverageThreshold) {
|
||||||
|
Set<CallableStatus> output = new HashSet<CallableStatus>();
|
||||||
|
|
||||||
|
// if too much coverage
|
||||||
|
if (getCoverage() > maximumCoverageThreshold)
|
||||||
|
output.add(CallableStatus.EXCESSIVE_COVERAGE);
|
||||||
|
|
||||||
|
// if not enough coverage
|
||||||
|
if (getCoverage() < minimumCoverageThreshold) {
|
||||||
|
// was there a lot of low Qual coverage?
|
||||||
|
if (getRawCoverage() >= minimumCoverageThreshold)
|
||||||
|
output.add(CallableStatus.POOR_QUALITY);
|
||||||
|
// no?
|
||||||
|
else {
|
||||||
|
// is there any coverage?
|
||||||
|
if (getRawCoverage() > 0)
|
||||||
|
output.add(CallableStatus.LOW_COVERAGE);
|
||||||
|
else
|
||||||
|
output.add(CallableStatus.NO_COVERAGE);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
return output;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,175 @@
|
||||||
|
/*
|
||||||
|
* Copyright (c) 2012, The Broad Institute
|
||||||
|
*
|
||||||
|
* Permission is hereby granted, free of charge, to any person
|
||||||
|
* obtaining a copy of this software and associated documentation
|
||||||
|
* files (the "Software"), to deal in the Software without
|
||||||
|
* restriction, including without limitation the rights to use,
|
||||||
|
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||||
|
* copies of the Software, and to permit persons to whom the
|
||||||
|
* Software is furnished to do so, subject to the following
|
||||||
|
* conditions:
|
||||||
|
*
|
||||||
|
* The above copyright notice and this permission notice shall be
|
||||||
|
* included in all copies or substantial portions of the Software.
|
||||||
|
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||||
|
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||||
|
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||||
|
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||||
|
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||||
|
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||||
|
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
||||||
|
* OTHER DEALINGS IN THE SOFTWARE.
|
||||||
|
*/
|
||||||
|
|
||||||
|
package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
|
||||||
|
|
||||||
|
import org.broadinstitute.sting.utils.GenomeLoc;
|
||||||
|
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
|
||||||
|
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
|
||||||
|
|
||||||
|
import java.util.*;
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Short one line description of the walker.
|
||||||
|
*
|
||||||
|
* @author Mauricio Carneiro
|
||||||
|
* @since 2/1/12
|
||||||
|
*/
|
||||||
|
class SampleStatistics {
|
||||||
|
private final GenomeLoc interval;
|
||||||
|
private final ArrayList<LocusStatistics> loci;
|
||||||
|
|
||||||
|
private final int minimumCoverageThreshold;
|
||||||
|
private final int maximumCoverageThreshold;
|
||||||
|
private final int minimumMappingQuality;
|
||||||
|
private final int minimumBaseQuality;
|
||||||
|
|
||||||
|
private int preComputedTotalCoverage = -1; // avoids re-calculating the total sum (-1 means we haven't pre-computed it yet)
|
||||||
|
|
||||||
|
private SampleStatistics(GenomeLoc interval, ArrayList<LocusStatistics> loci, int minimumCoverageThreshold, int maximumCoverageThreshold, int minimumMappingQuality, int minimumBaseQuality) {
|
||||||
|
this.interval = interval;
|
||||||
|
this.loci = loci;
|
||||||
|
this.minimumCoverageThreshold = minimumCoverageThreshold;
|
||||||
|
this.maximumCoverageThreshold = maximumCoverageThreshold;
|
||||||
|
this.minimumMappingQuality = minimumMappingQuality;
|
||||||
|
this.minimumBaseQuality = minimumBaseQuality;
|
||||||
|
}
|
||||||
|
|
||||||
|
public SampleStatistics(GenomeLoc interval, int minimumCoverageThreshold, int maximumCoverageThreshold, int minimumMappingQuality, int minimumBaseQuality) {
|
||||||
|
this(interval, new ArrayList<LocusStatistics>(interval.size()), minimumCoverageThreshold, maximumCoverageThreshold, minimumMappingQuality, minimumBaseQuality);
|
||||||
|
|
||||||
|
// Initialize every loci (this way we don't have to worry about non-existent loci in the object
|
||||||
|
for (int i = 0; i < interval.size(); i++)
|
||||||
|
this.loci.add(i, new LocusStatistics());
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
public long totalCoverage() {
|
||||||
|
if (preComputedTotalCoverage < 0)
|
||||||
|
calculateTotalCoverage();
|
||||||
|
return preComputedTotalCoverage;
|
||||||
|
}
|
||||||
|
|
||||||
|
public double averageCoverage() {
|
||||||
|
if (preComputedTotalCoverage < 0)
|
||||||
|
calculateTotalCoverage();
|
||||||
|
return (double) preComputedTotalCoverage / loci.size();
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Calculates the callable statuses of the entire interval
|
||||||
|
*
|
||||||
|
* @return the callable statuses of the entire interval
|
||||||
|
*/
|
||||||
|
public Set<CallableStatus> getCallableStatuses() {
|
||||||
|
|
||||||
|
Map<CallableStatus, Integer> totals = new HashMap<CallableStatus, Integer>(CallableStatus.values().length);
|
||||||
|
|
||||||
|
// initialize map
|
||||||
|
for (CallableStatus status : CallableStatus.values())
|
||||||
|
totals.put(status, 0);
|
||||||
|
|
||||||
|
// sum up all the callable statuses for each locus
|
||||||
|
for (int i = 0; i < interval.size(); i++) {
|
||||||
|
for (CallableStatus status : callableStatus(i)) {
|
||||||
|
int count = totals.get(status);
|
||||||
|
|
||||||
|
totals.put(status, count + 1);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
Set<CallableStatus> output = new HashSet<CallableStatus>();
|
||||||
|
|
||||||
|
// double to avoid type casting
|
||||||
|
double intervalSize = interval.size();
|
||||||
|
|
||||||
|
double coverageStatusThreshold = 0.20;
|
||||||
|
if ((totals.get(CallableStatus.NO_COVERAGE) / intervalSize) > coverageStatusThreshold)
|
||||||
|
output.add(CallableStatus.NO_COVERAGE);
|
||||||
|
|
||||||
|
if ((totals.get(CallableStatus.LOW_COVERAGE) / intervalSize) > coverageStatusThreshold)
|
||||||
|
output.add(CallableStatus.LOW_COVERAGE);
|
||||||
|
|
||||||
|
double excessiveCoverageThreshold = 0.20;
|
||||||
|
if ((totals.get(CallableStatus.EXCESSIVE_COVERAGE) / intervalSize) > excessiveCoverageThreshold)
|
||||||
|
output.add(CallableStatus.EXCESSIVE_COVERAGE);
|
||||||
|
|
||||||
|
double qualityStatusThreshold = 0.50;
|
||||||
|
if ((totals.get(CallableStatus.POOR_QUALITY) / intervalSize) > qualityStatusThreshold)
|
||||||
|
output.add(CallableStatus.POOR_QUALITY);
|
||||||
|
|
||||||
|
if (totals.get(CallableStatus.REF_N) > 0)
|
||||||
|
output.add(CallableStatus.REF_N);
|
||||||
|
|
||||||
|
if (output.isEmpty()) {
|
||||||
|
output.add(CallableStatus.PASS);
|
||||||
|
}
|
||||||
|
return output;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Adds a locus to the interval wide stats
|
||||||
|
*
|
||||||
|
* @param locus The locus given as a GenomeLoc
|
||||||
|
* @param pileup The pileup of that locus
|
||||||
|
*/
|
||||||
|
public void addLocus(GenomeLoc locus, ReadBackedPileup pileup) {
|
||||||
|
if (!interval.containsP(locus))
|
||||||
|
throw new ReviewedStingException(String.format("Locus %s is not part of the Interval", locus));
|
||||||
|
|
||||||
|
// a null pileup means there nothing ot add
|
||||||
|
if (pileup != null) {
|
||||||
|
|
||||||
|
int locusIndex = locus.getStart() - interval.getStart();
|
||||||
|
|
||||||
|
int rawCoverage = pileup.depthOfCoverage();
|
||||||
|
int coverage = pileup.getBaseAndMappingFilteredPileup(minimumBaseQuality, minimumMappingQuality).depthOfCoverage();
|
||||||
|
|
||||||
|
LocusStatistics locusData = new LocusStatistics(coverage, rawCoverage);
|
||||||
|
|
||||||
|
loci.add(locusIndex, locusData);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* returns the callable status of this locus without taking the reference base into account.
|
||||||
|
*
|
||||||
|
* @param locusIndex location in the genome to inquire (only one locus)
|
||||||
|
* @return the callable status of a locus
|
||||||
|
*/
|
||||||
|
private Set<CallableStatus> callableStatus(int locusIndex) {
|
||||||
|
LocusStatistics locus = loci.get(locusIndex);
|
||||||
|
|
||||||
|
return locus.callableStatuses(minimumCoverageThreshold, maximumCoverageThreshold);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
private void calculateTotalCoverage() {
|
||||||
|
preComputedTotalCoverage = 0;
|
||||||
|
for (LocusStatistics locus : loci)
|
||||||
|
preComputedTotalCoverage += locus.getCoverage();
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
Loading…
Reference in New Issue