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Removing these utilities as part of a hostage negotation with Matt. Can I have my journal club paper now?! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3539 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2010-06-11 21:41:29 +00:00
parent c0370f4d0a
commit 804facb0cc
3 changed files with 0 additions and 112 deletions
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29
build.xml
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@ -175,24 +175,6 @@
</manifest>
</jar>
<jar jarfile="${dist.dir}/MarkAllAlignmentsAsPrimary.jar" whenmanifestonly="skip">
<fileset dir="build">
<include name="**/*.class" />
</fileset>
<manifest>
<attribute name="Main-Class" value="org.broadinstitute.sting.oneoffprojects.tools.MarkAllAlignmentsAsPrimary" />
</manifest>
</jar>
<jar jarfile="${dist.dir}/RepairSeattleBAM.jar" whenmanifestonly="skip">
<fileset dir="build">
<include name="**/*.class" />
</fileset>
<manifest>
<attribute name="Main-Class" value="org.broadinstitute.sting.oneoffprojects.tools.RepairSeattleBAM" />
</manifest>
</jar>
<jar jarfile="${dist.dir}/VCFTool.jar" whenmanifestonly="skip">
<fileset dir="build">
<include name="**/*.class"/>
@ -238,17 +220,6 @@
</manifest>
</jar>
<jar jarfile="${dist.dir}/MarkAllAlignmentsAsPrimary.jar" update="true" whenmanifestonly="skip">
<manifest>
<attribute name="Class-Path" value="${jar.classpath}" />
</manifest>
</jar>
<jar jarfile="${dist.dir}/RepairSeattleBAM.jar" update="true" whenmanifestonly="skip">
<manifest>
<attribute name="Class-Path" value="${jar.classpath}" />
</manifest>
</jar>
</target>
<target name="core" description="force a build of the Sting core code">

39
java/src/org/broadinstitute/sting/oneoffprojects/tools/MarkAllAlignmentsAsPrimary.java
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@ -1,39 +0,0 @@
package org.broadinstitute.sting.oneoffprojects.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 net.sf.samtools.SAMFileWriter;
import net.sf.samtools.SAMFileWriterFactory;
import java.io.*;
public class MarkAllAlignmentsAsPrimary extends CommandLineProgram {
@Usage(programVersion="1.0") public String USAGE = "Mark all alignments as primary.";
@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 (bam or sam).",
optional=true) public File OUT = null;
public static void main(final String[] argv) {
System.exit(new MarkAllAlignmentsAsPrimary().instanceMain(argv));
}
protected int doWork() {
SAMFileReader inReader = new SAMFileReader(IN);
SAMFileWriter outWriter = (new SAMFileWriterFactory()).makeSAMOrBAMWriter(inReader.getFileHeader(), true, OUT);
for (SAMRecord read : inReader ) {
read.setNotPrimaryAlignmentFlag(false);
outWriter.addAlignment(read);
}
inReader.close();
outWriter.close();
return 0;
}
}

44
java/src/org/broadinstitute/sting/oneoffprojects/tools/RepairSeattleBAM.java
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@ -1,44 +0,0 @@
package org.broadinstitute.sting.oneoffprojects.tools;
import net.sf.picard.cmdline.CommandLineProgram;
import net.sf.picard.cmdline.Usage;
import net.sf.picard.cmdline.Option;
import net.sf.samtools.*;
import java.io.*;
public class RepairSeattleBAM extends CommandLineProgram {
@Usage(programVersion="1.0") public String USAGE = "Fix read group info";
@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 (bam or sam).",
optional=true) public File OUT = null;
@Option(shortName="S",doc="Sample.",
optional=true) public String SAMPLE = null;
public static void main(final String[] argv) {
System.exit(new RepairSeattleBAM().instanceMain(argv));
}
protected int doWork() {
SAMFileReader inReader = new SAMFileReader(IN);
for (SAMReadGroupRecord rg : inReader.getFileHeader().getReadGroups()) {
rg.setSample(SAMPLE);
}
SAMFileWriter outWriter = (new SAMFileWriterFactory()).makeSAMOrBAMWriter(inReader.getFileHeader(), true, OUT);
for (SAMRecord read : inReader ) {
//read.getReadGroup().setSample(SAMPLE);
read.setAttribute("SM", SAMPLE);
outWriter.addAlignment(read);
}
inReader.close();
outWriter.close();
return 0;
}
}