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1. Rename SetNmAndUqTags to SetNmMDAndUqTags. 2. Fixes: #622
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,113 @@ | ||
| /* | ||
| * 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; | ||
|
|
||
| import htsjdk.samtools.SAMException; | ||
| import htsjdk.samtools.SAMFileHeader; | ||
| import htsjdk.samtools.SAMFileWriter; | ||
| import htsjdk.samtools.SAMFileWriterFactory; | ||
| import htsjdk.samtools.SamReader; | ||
| import htsjdk.samtools.SamReaderFactory; | ||
| import htsjdk.samtools.reference.ReferenceSequenceFileWalker; | ||
| import htsjdk.samtools.util.CloserUtil; | ||
| import htsjdk.samtools.util.IOUtil; | ||
| import htsjdk.samtools.util.Log; | ||
| import htsjdk.samtools.util.ProgressLogger; | ||
| import picard.cmdline.CommandLineProgram; | ||
| import picard.cmdline.CommandLineProgramProperties; | ||
| import picard.cmdline.Option; | ||
| import picard.cmdline.StandardOptionDefinitions; | ||
| import picard.cmdline.programgroups.SamOrBam; | ||
|
|
||
| import java.io.File; | ||
| import java.util.stream.StreamSupport; | ||
|
|
||
| /** | ||
| * @author Yossi Farjoun | ||
| */ | ||
| @CommandLineProgramProperties( | ||
| usage = SetNmMdAndUqTags.USAGE_SUMMARY + SetNmMdAndUqTags.USAGE_DETAILS, | ||
| usageShort = SetNmMdAndUqTags.USAGE_SUMMARY, | ||
| programGroup = SamOrBam.class | ||
| ) | ||
| public class SetNmMdAndUqTags extends CommandLineProgram { | ||
| static final String USAGE_SUMMARY = "Fixes the NM, MD, and UQ tags in a SAM file. "; | ||
| static final String USAGE_DETAILS = "This tool takes in a SAM or BAM file (sorted by coordinate) and calculates the NM, MD, and UQ tags by comparing with the reference."+ | ||
| "<br />" + | ||
| "This may be needed when MergeBamAlignment was run with SORT_ORDER different from 'coordinate' and thus could not fix\n"+ | ||
| "these tags then.<br />"+ | ||
| "<h4>Usage example:</h4>" + | ||
| "<pre>" + | ||
| "java -jar picard.jar SetNmMDAndUqTags \\<br />" + | ||
| " I=sorted.bam \\<br />" + | ||
| " O=fixed.bam \\<br />"+ | ||
| "</pre>" + | ||
| "<hr />"; | ||
| @Option(doc = "The BAM or SAM file to fix.", shortName = StandardOptionDefinitions.INPUT_SHORT_NAME) | ||
| public File INPUT; | ||
|
|
||
| @Option(doc = "The fixed BAM or SAM output file. ", shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME) | ||
| public File OUTPUT; | ||
|
|
||
| @Option(doc = "Whether the file contains bisulfite sequence (used when calculating the NM tag).") | ||
| public boolean IS_BISULFITE_SEQUENCE = false; | ||
|
|
||
| @Override | ||
| protected String[] customCommandLineValidation() { | ||
| if (REFERENCE_SEQUENCE == null) { | ||
| return new String[]{"Must have a non-null REFERENCE_SEQUENCE"}; | ||
| } | ||
| return super.customCommandLineValidation(); | ||
| } | ||
|
|
||
| private final Log log = Log.getInstance(SetNmMdAndUqTags.class); | ||
|
|
||
| public static void main(final String[] argv) { | ||
| new SetNmMdAndUqTags().instanceMainWithExit(argv); | ||
| } | ||
|
|
||
| protected int doWork() { | ||
| IOUtil.assertFileIsReadable(INPUT); | ||
| IOUtil.assertFileIsWritable(OUTPUT); | ||
| final SamReader reader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(INPUT); | ||
|
|
||
| if (reader.getFileHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate) { | ||
| throw new SAMException("Input must be coordinate-sorted for this program to run. Found: " + reader.getFileHeader().getSortOrder()); | ||
| } | ||
|
|
||
| final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), true, OUTPUT); | ||
| writer.setProgressLogger( | ||
| new ProgressLogger(log, (int) 1e7, "Wrote", "records")); | ||
|
|
||
| final ReferenceSequenceFileWalker refSeq = new ReferenceSequenceFileWalker(REFERENCE_SEQUENCE); | ||
|
|
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| StreamSupport.stream(reader.spliterator(),false) | ||
| .peek(rec->{if(!rec.getReadUnmappedFlag()) AbstractAlignmentMerger.fixNmMdAndUq(rec, refSeq, IS_BISULFITE_SEQUENCE);}) | ||
| .forEach(writer::addAlignment); | ||
|
|
||
| CloserUtil.close(reader); | ||
| writer.close(); | ||
| return 0; | ||
| } | ||
| } |
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