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Optional flag to add an attribute in the SAM/BAM file used to store t…
…he size of a duplicate set. A separate attribute is also added to store which read was selected as representative out of a duplicate set.
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| rootProject.name = "picard" | ||
| include 'picard_gradle_v2' | ||
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79 changes: 79 additions & 0 deletions
79
src/main/java/picard/sam/markduplicates/util/RepresentativeReadIndexerCodec.java
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| /* | ||
| * The MIT License | ||
| * | ||
| * Copyright (c) 2016 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 picard.sam.markduplicates.util; | ||
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| import htsjdk.samtools.util.SortingCollection; | ||
| import picard.PicardException; | ||
| import picard.sam.util.RepresentativeReadIndexer; | ||
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| import java.io.*; | ||
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| /** Codec for read names and integers that outputs the primitive fields and reads them back. */ | ||
| public class RepresentativeReadIndexerCodec implements SortingCollection.Codec<RepresentativeReadIndexer> { | ||
| protected DataInputStream in; | ||
| protected DataOutputStream out; | ||
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| public SortingCollection.Codec<RepresentativeReadIndexer> clone() { | ||
| return new RepresentativeReadIndexerCodec(); | ||
| } | ||
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| public void setOutputStream(final OutputStream os) { this.out = new DataOutputStream(os); } | ||
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| public void setInputStream(final InputStream is) { this.in = new DataInputStream(is); } | ||
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| public DataInputStream getInputStream() { | ||
| return in; | ||
| } | ||
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| public DataOutputStream getOutputStream() { | ||
| return out; | ||
| } | ||
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| public void encode(final RepresentativeReadIndexer rni) { | ||
| try { | ||
| this.out.writeInt(rni.readIndexInFile); | ||
| this.out.writeInt(rni.setSize); | ||
| this.out.writeInt(rni.representativeReadIndexInFile); | ||
| } catch (final IOException ioe) { | ||
| throw new PicardException("Exception writing ReadEnds to file.", ioe); | ||
| } | ||
| } | ||
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| public RepresentativeReadIndexer decode() { | ||
| final RepresentativeReadIndexer rni = new RepresentativeReadIndexer(); | ||
| try { | ||
| // If the first read results in an EOF we've exhausted the stream | ||
| try { | ||
| rni.readIndexInFile = this.in.readInt(); | ||
| } catch (final EOFException eof) { | ||
| return null; | ||
| } | ||
| rni.setSize = this.in.readInt(); | ||
| rni.representativeReadIndexInFile = this.in.readInt(); | ||
| return rni; | ||
| } catch (final IOException ioe) { | ||
| throw new PicardException("Exception writing ReadEnds to file.", ioe); | ||
| } | ||
| } | ||
| } |
11 changes: 11 additions & 0 deletions
11
src/main/java/picard/sam/util/RepresentativeReadIndexer.java
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| package picard.sam.util; | ||
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| /** | ||
| * Little struct-like class to hold a record index, the index of the corresponding representative read, and duplicate set size information. | ||
| */ | ||
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| public class RepresentativeReadIndexer { | ||
| public int readIndexInFile = -1; | ||
| public int setSize = -1; | ||
| public int representativeReadIndexInFile = -1; | ||
| } |
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