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cleaned up the PrintReadsWalker, and added a lot of documentation. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@952 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-06-09 14:28:32 +00:00
parent b45b1d5f2b
commit bf6190b471
1 changed files with 61 additions and 9 deletions
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70
java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
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@ -11,27 +11,74 @@ import java.io.FileNotFoundException;
import java.io.File;
import java.util.Random;
/*
* Copyright (c) 2009 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.
*/
/**
* This walker prints out the reads from the BAM files provided to the traversal engines.
* It also supports the command line option '-outputBamFile filname', which outputs all the
* reads to a specified BAM file
*/
public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
@Argument(fullName="outputBamFile", shortName="of", doc="Write output to this BAM filename instead of STDOUT", required=false)
/** an optional argument to dump the reads out to a BAM file */
@Argument(fullName = "outputBamFile", shortName = "of", doc = "Write output to this BAM filename instead of STDOUT", required = false)
String outputBamFile = null;
public SAMRecord map(char[] ref, SAMRecord read) {
/**
* The reads map function.
* @param ref the reference bases that correspond to our read, if a reference was provided
* @param read the read itself, as a SAMRecord
* @return the read itself
*/
public SAMRecord map( char[] ref, SAMRecord read ) {
return read;
}
/**
* reduceInit is called once before any calls to the map function. We use it here to setup the output
* bam file, if it was specified on the command line
* @return SAMFileWriter, set to the BAM output file if the command line option was set, null otherwise
*/
public SAMFileWriter reduceInit() {
if ( outputBamFile != null ) { // ! outputBamFile.equals("") ) {
if (outputBamFile != null) {
SAMFileHeader header = this.getToolkit().getEngine().getSAMHeader();
return Utils.createSAMFileWriterWithCompression(header, true, outputBamFile, getToolkit().getBAMCompression());
}
else {
} else {
return null;
}
}
public SAMFileWriter reduce(SAMRecord read, SAMFileWriter output) {
if ( output != null ) {
/**
* given a read and a output location, reduce by emitting the read
* @param read the read itself
* @param output the output source
* @return the SAMFileWriter, so that the next reduce can emit to the same source
*/
public SAMFileWriter reduce( SAMRecord read, SAMFileWriter output ) {
if (output != null) {
output.addAlignment(read);
} else {
out.println(read.format());
@ -40,8 +87,13 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
return output;
}
public void onTraversalDone(SAMFileWriter output) {
if ( output != null ) {
/**
* when we're done traversing, close the reads file
* @param output the SAMFileWriter we've used in the reduce phase
*/
public void onTraversalDone( SAMFileWriter output ) {
if (output != null) {
output.close();
}
}