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
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/*
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* Copyright (c) 2010 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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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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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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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
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.walkers.fasta;
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import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.ReadWalker;
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import org.broadinstitute.sting.gatk.walkers.WalkerName;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.utils.BaseUtils;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.Output;
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import net.sf.samtools.SAMRecord;
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import java.io.*;
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/**
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* Converts reads from the input BAM file into fastq format, stripping away all alignment information.
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* Optionally re-reverses the negative strand alignments using the --re-reverse command-line argument.
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*/
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@WalkerName("BamToFastq")
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public class BamToFastqWalker extends ReadWalker<Integer, Integer> {
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@Output
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private PrintStream out;
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@Argument(fullName="re_reverse", shortName="reverse", doc="re-reverse bases and quals of reads from the negative strand", required=false)
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private Boolean RE_REVERSE = false;
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@Argument(fullName="SQFile", shortName="SQ", doc="Output path for secondary quality map (readName => SAM SQ field)", required=false)
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String SQFile = null;
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private PrintWriter sqbw = null;
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public void initialize() {
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if ( SQFile != null ) {
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try {
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sqbw = new PrintWriter(SQFile);
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} catch (IOException e) {
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throw new RuntimeException("Unable to open sq output file: " + SQFile);
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}
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}
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}
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public Integer map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
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out.println("@" + read.getReadName());
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if ( !RE_REVERSE || !read.getReadNegativeStrandFlag() ) {
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out.println(read.getReadString());
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out.println("+");
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out.println(read.getBaseQualityString());
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} else {
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out.println(BaseUtils.simpleReverseComplement(read.getReadString()));
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out.println("+");
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out.println(Utils.reverse(read.getBaseQualityString()));
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}
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if ( sqbw != null ) {
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byte[] sqs = (byte[])read.getAttribute("SQ");
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if ( sqs != null ) {
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sqbw.print(read.getReadName() + "\t" + "SQ:H:");
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for ( byte sq : sqs ) {
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sqbw.printf("%02X", sq);
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}
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sqbw.println();
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}
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}
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return 1;
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}
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public Integer reduceInit() {
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return 0;
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}
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public Integer reduce(Integer value, Integer sum) {
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return value + sum;
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}
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public void onTraversalDone(Integer sum) {
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if ( sqbw != null )
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sqbw.close();
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logger.info("Number of reads converted: " + sum);
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}
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}
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package org.broadinstitute.sting.playground.tools;
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import net.sf.picard.cmdline.CommandLineProgram;
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import net.sf.picard.cmdline.Usage;
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import net.sf.picard.cmdline.Option;
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import net.sf.samtools.SAMFileReader;
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import net.sf.samtools.SAMRecord;
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import java.io.*;
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import org.broadinstitute.sting.utils.BaseUtils;
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import org.broadinstitute.sting.utils.Utils;
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/**
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* Created by IntelliJ IDEA.
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* User: asivache
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* Date: Aug 12, 2009
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* Time: 3:24:46 PM
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* To change this template use File | Settings | File Templates.
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*/
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public class BamToFastq extends CommandLineProgram {
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@Usage(programVersion="1.0") public String USAGE = "Extracts read sequences and qualities from the input sam/bam file and wirtes them into "+
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"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, "+
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"the read's sequence from input sam file will be reverse-complemented prior to writing it to fastq in order restore correctly "+
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"the original read sequence as it was generated by the sequencer.";
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@Option(shortName="I", doc="Input file (bam or sam) to extract reads from. If not specified, reads from stdin.",
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optional=true) public File IN = null;
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@Option(shortName="O",doc="Output file (fastq). If not specified, output is printed to stdout.",
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optional=true) public File OUT = null;
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@Option(shortName="RC", doc="re-reverse bases and quals of reads aligned to the negative strand before writing them to fastq", optional=true)
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public Boolean RE_REVERSE = true;
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public static void main(final String[] argv) {
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System.exit(new BamToFastq().instanceMain(argv));
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}
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protected int doWork() {
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InputStream ins = null;
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if ( IN == null ) ins = System.in;
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else {
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try {
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ins = new FileInputStream(IN);
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} catch ( FileNotFoundException ie ) {
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System.out.println("Failed to open input file "+IN+": "+ie.getCause());
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return 1;
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}
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}
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SAMFileReader inReader = new SAMFileReader(ins);
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PrintStream out = null;
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if ( OUT == null ) out = System.out;
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else {
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try {
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out = new PrintStream(OUT);
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} catch ( FileNotFoundException ie ) {
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System.out.println("Failed to open output file "+OUT+": "+ie.getCause());
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return 1;
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}
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}
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for (SAMRecord read : inReader ) {
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out.println("@" + read.getReadName());
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if ( read.getReadUnmappedFlag() || !RE_REVERSE || !read.getReadNegativeStrandFlag() ) {
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out.println(read.getReadString());
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out.println('+');
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out.println(read.getBaseQualityString());
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} else {
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out.println(BaseUtils.simpleReverseComplement(read.getReadString()));
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out.println('+');
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out.println(Utils.reverse(read.getBaseQualityString()));
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}
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}
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inReader.close();
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out.close();
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return 0;
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}
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}
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package org.broadinstitute.sting.gatk.walkers.fasta;
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import org.broadinstitute.sting.WalkerTest;
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import org.junit.Test;
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import java.util.Arrays;
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public class BamToFastqIntegrationTest extends WalkerTest {
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@Test
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public void testIntervals() {
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WalkerTestSpec spec1 = new WalkerTestSpec(
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"-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",
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1,
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Arrays.asList("49431d567524d6fd32a569504b25f212"));
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executeTest("testBamToFasta", spec1);
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WalkerTestSpec spec2 = new WalkerTestSpec(
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"-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",
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1,
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Arrays.asList("f3a4a39d36270136c12bb1315fdb7dff"));
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executeTest("testBamToFastaReverse", spec2);
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}
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}
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