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I just spoke to Andrey & Kiran (the original authors of these tools), and they voted to kill these in favor of Picard 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4313 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-09-20 13:27:35 +00:00
parent b24172c80f
commit f5a30d0248
3 changed files with 0 additions and 212 deletions
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106
java/src/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqWalker.java
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@ -1,106 +0,0 @@
/*
* Copyright (c) 2010 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.fasta;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import net.sf.samtools.SAMRecord;
import java.io.*;
/**
* Converts reads from the input BAM file into fastq format, stripping away all alignment information.
* Optionally re-reverses the negative strand alignments using the --re-reverse command-line argument.
*/
@WalkerName("BamToFastq")
public class BamToFastqWalker extends ReadWalker<Integer, Integer> {
@Output
private PrintStream out;
@Argument(fullName="re_reverse", shortName="reverse", doc="re-reverse bases and quals of reads from the negative strand", required=false)
private Boolean RE_REVERSE = false;
@Argument(fullName="SQFile", shortName="SQ", doc="Output path for secondary quality map (readName => SAM SQ field)", required=false)
String SQFile = null;
private PrintWriter sqbw = null;
public void initialize() {
if ( SQFile != null ) {
try {
sqbw = new PrintWriter(SQFile);
} catch (IOException e) {
throw new RuntimeException("Unable to open sq output file: " + SQFile);
}
}
}
public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
out.println("@" + read.getReadName());
if ( !RE_REVERSE || !read.getReadNegativeStrandFlag() ) {
out.println(read.getReadString());
out.println("+");
out.println(read.getBaseQualityString());
} else {
out.println(BaseUtils.simpleReverseComplement(read.getReadString()));
out.println("+");
out.println(Utils.reverse(read.getBaseQualityString()));
}
if ( sqbw != null ) {
byte[] sqs = (byte[])read.getAttribute("SQ");
if ( sqs != null ) {
sqbw.print(read.getReadName() + "\t" + "SQ:H:");
for ( byte sq : sqs ) {
sqbw.printf("%02X", sq);
}
sqbw.println();
}
}
return 1;
}
public Integer reduceInit() {
return 0;
}
public Integer reduce(Integer value, Integer sum) {
return value + sum;
}
public void onTraversalDone(Integer sum) {
if ( sqbw != null )
sqbw.close();
logger.info("Number of reads converted: " + sum);
}
}

82
java/src/org/broadinstitute/sting/playground/tools/BamToFastq.java
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@ -1,82 +0,0 @@
package org.broadinstitute.sting.playground.tools;
import net.sf.picard.cmdline.CommandLineProgram;
import net.sf.picard.cmdline.Usage;
import net.sf.picard.cmdline.Option;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMRecord;
import java.io.*;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.Utils;
/**
* Created by IntelliJ IDEA.
* User: asivache
* Date: Aug 12, 2009
* Time: 3:24:46 PM
* To change this template use File | Settings | File Templates.
*/
public class BamToFastq extends CommandLineProgram {
@Usage(programVersion="1.0") public String USAGE = "Extracts read sequences and qualities from the input sam/bam file and wirtes them into "+
"the output file in fastq format. In the RC mode (default is True), if the read is aligned and the alignment is to the reverse strand on the genome, "+
"the read's sequence from input sam file will be reverse-complemented prior to writing it to fastq in order restore correctly "+
"the original read sequence as it was generated by the sequencer.";
@Option(shortName="I", doc="Input file (bam or sam) to extract reads from. If not specified, reads from stdin.",
optional=true) public File IN = null;
@Option(shortName="O",doc="Output file (fastq). If not specified, output is printed to stdout.",
optional=true) public File OUT = null;
@Option(shortName="RC", doc="re-reverse bases and quals of reads aligned to the negative strand before writing them to fastq", optional=true)
public Boolean RE_REVERSE = true;
public static void main(final String[] argv) {
System.exit(new BamToFastq().instanceMain(argv));
}
protected int doWork() {
InputStream ins = null;
if ( IN == null ) ins = System.in;
else {
try {
ins = new FileInputStream(IN);
} catch ( FileNotFoundException ie ) {
System.out.println("Failed to open input file "+IN+": "+ie.getCause());
return 1;
}
}
SAMFileReader inReader = new SAMFileReader(ins);
PrintStream out = null;
if ( OUT == null ) out = System.out;
else {
try {
out = new PrintStream(OUT);
} catch ( FileNotFoundException ie ) {
System.out.println("Failed to open output file "+OUT+": "+ie.getCause());
return 1;
}
}
for (SAMRecord read : inReader ) {
out.println("@" + read.getReadName());
if ( read.getReadUnmappedFlag() || !RE_REVERSE || !read.getReadNegativeStrandFlag() ) {
out.println(read.getReadString());
out.println('+');
out.println(read.getBaseQualityString());
} else {
out.println(BaseUtils.simpleReverseComplement(read.getReadString()));
out.println('+');
out.println(Utils.reverse(read.getBaseQualityString()));
}
}
inReader.close();
out.close();
return 0;
}
}

24
java/test/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqIntegrationTest.java
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package org.broadinstitute.sting.gatk.walkers.fasta;
import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;
import java.util.Arrays;
public class BamToFastqIntegrationTest extends WalkerTest {
@Test
public void testIntervals() {
WalkerTestSpec spec1 = new WalkerTestSpec(
"-T BamToFastq -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,100-10,000,500;1:10,100,000-10,101,000;1:10,900,000-10,900,001 -o %s",
1,
Arrays.asList("49431d567524d6fd32a569504b25f212"));
executeTest("testBamToFasta", spec1);
WalkerTestSpec spec2 = new WalkerTestSpec(
"-T BamToFastq -reverse -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,100-10,000,500;1:10,100,000-10,101,000;1:10,900,000-10,900,001 -o %s",
1,
Arrays.asList("f3a4a39d36270136c12bb1315fdb7dff"));
executeTest("testBamToFastaReverse", spec2);
}
}