This is, strictly speaking, NOT a GATK module. Standalone, picard-level executable except that it uses couple of gatk utils (GenomeLoc). Remaps alignments from cutom reference (such as transcritome, hyb-sel etc) onto the 'master' reference
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1107 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache
parent
ee2af3b423
commit
73caf5db15
|
|
@ -0,0 +1,194 @@
|
||||||
|
package org.broadinstitute.sting.playground.utils;
|
||||||
|
|
||||||
|
import java.io.File;
|
||||||
|
import java.util.Comparator;
|
||||||
|
import java.util.Set;
|
||||||
|
import java.util.TreeSet;
|
||||||
|
import java.util.Map.Entry;
|
||||||
|
|
||||||
|
import org.broadinstitute.sting.utils.GenomeLocParser;
|
||||||
|
|
||||||
|
import net.sf.picard.cmdline.CommandLineProgram;
|
||||||
|
import net.sf.picard.cmdline.Option;
|
||||||
|
import net.sf.picard.cmdline.Usage;
|
||||||
|
import net.sf.picard.reference.ReferenceSequenceFileWalker;
|
||||||
|
import net.sf.samtools.SAMFileHeader;
|
||||||
|
import net.sf.samtools.SAMFileReader;
|
||||||
|
import net.sf.samtools.SAMFileWriter;
|
||||||
|
import net.sf.samtools.SAMFileWriterFactory;
|
||||||
|
import net.sf.samtools.SAMRecord;
|
||||||
|
import net.sf.samtools.SAMFileHeader.SortOrder;
|
||||||
|
import net.sf.samtools.SAMFileReader.ValidationStringency;
|
||||||
|
|
||||||
|
|
||||||
|
public class RemapAlignments extends CommandLineProgram {
|
||||||
|
|
||||||
|
// Usage and parameters
|
||||||
|
@Usage(programVersion="1.0") public String USAGE = "Investigates indels called in the alignment data\n";
|
||||||
|
@Option(shortName="M",
|
||||||
|
doc="Map file: from the reference the reads were aligned to, to the master reference the alignments should be remapped to",
|
||||||
|
optional=false)
|
||||||
|
public File MAP_FILE = null;
|
||||||
|
@Option(shortName="I",
|
||||||
|
doc="Input file (bam or sam) with alignments to be remapped",
|
||||||
|
optional=false)
|
||||||
|
public File IN = null;
|
||||||
|
@Option(shortName="O",
|
||||||
|
doc="File to write remapped reads to.",
|
||||||
|
optional=false)
|
||||||
|
public File OUT = null;
|
||||||
|
@Option(shortName="R",
|
||||||
|
doc="Reference to remap alignments onto.",
|
||||||
|
optional=false)
|
||||||
|
public File REFERENCE = null;
|
||||||
|
@Option(
|
||||||
|
doc="If a read has multiple alignments that are exactly the same after remapping, "+
|
||||||
|
"keep only one copy of such alignment in output file. Multiple alignments that are "+
|
||||||
|
"not equivalent after remaping are not affected by this flag. "+
|
||||||
|
"Multiple alignments for the same query must be grouped on adjacent lines of the input file to be detected," +
|
||||||
|
"otherwise REDUCE will have no effect.",
|
||||||
|
optional=true)
|
||||||
|
public boolean REDUCE = false;
|
||||||
|
|
||||||
|
|
||||||
|
private GenomicMap map = null;
|
||||||
|
private String lastReadName = null;
|
||||||
|
private int totalReads = 0;
|
||||||
|
private int totalRecords = 0;
|
||||||
|
private int badRecords = 0;
|
||||||
|
private int totalUnmappedReads = 0;
|
||||||
|
private int writtenRecords = 0;
|
||||||
|
|
||||||
|
private Set<SAMRecord> remappedReads = null;
|
||||||
|
private SAMFileWriter writer = null;
|
||||||
|
private SAMFileReader reader = null;
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/** Required main method implementation. */
|
||||||
|
public static void main(final String[] argv) {
|
||||||
|
System.exit(new RemapAlignments().instanceMain(argv));
|
||||||
|
}
|
||||||
|
|
||||||
|
protected int doWork() {
|
||||||
|
|
||||||
|
reader = new SAMFileReader(IN);
|
||||||
|
reader.setValidationStringency(ValidationStringency.SILENT);
|
||||||
|
SAMFileHeader oldHeader = reader.getFileHeader();
|
||||||
|
if ( oldHeader == null ) throw new RuntimeException("Failed to retrieve SAM file header from the input bam file");
|
||||||
|
|
||||||
|
if ( REDUCE && oldHeader.getSortOrder() != SortOrder.queryname )
|
||||||
|
System.out.println("WARNING: Input file is not sorted by query name, REDUCE may have no effect. Sort order: "
|
||||||
|
+oldHeader.getSortOrder());
|
||||||
|
|
||||||
|
remappedReads = new TreeSet<SAMRecord>(new AlignmentComparator());
|
||||||
|
|
||||||
|
SAMFileHeader h = new SAMFileHeader();
|
||||||
|
|
||||||
|
for ( Entry<String, Object> attr : oldHeader.getAttributes() ) h.setAttribute(attr.getKey(), attr.getValue());
|
||||||
|
h.setGroupOrder(oldHeader.getGroupOrder());
|
||||||
|
h.setProgramRecords(oldHeader.getProgramRecords());
|
||||||
|
h.setReadGroups(oldHeader.getReadGroups());
|
||||||
|
|
||||||
|
if ( oldHeader.getSortOrder() == SortOrder.queryname ) {
|
||||||
|
h.setSortOrder(SortOrder.queryname);
|
||||||
|
} else {
|
||||||
|
h.setSortOrder(SortOrder.unsorted);
|
||||||
|
}
|
||||||
|
|
||||||
|
ReferenceSequenceFileWalker reference = new ReferenceSequenceFileWalker(REFERENCE);
|
||||||
|
|
||||||
|
if ( reference.getSequenceDictionary() == null ) {
|
||||||
|
System.out.println("No reference sequence dictionary found. Aborting.");
|
||||||
|
reader.close();
|
||||||
|
System.exit(1);
|
||||||
|
}
|
||||||
|
|
||||||
|
h.setSequenceDictionary(reference.getSequenceDictionary());
|
||||||
|
GenomeLocParser.setupRefContigOrdering(reference.getSequenceDictionary());
|
||||||
|
|
||||||
|
map = new GenomicMap(10000);
|
||||||
|
map.read(MAP_FILE);
|
||||||
|
System.out.println("Map loaded successfully: "+map.size()+" contigs");
|
||||||
|
|
||||||
|
|
||||||
|
writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(h, true, OUT);
|
||||||
|
|
||||||
|
for ( SAMRecord read : reader ) {
|
||||||
|
|
||||||
|
|
||||||
|
if ( map.remapToMasterReference(read,h,true) == null ) {
|
||||||
|
badRecords++;
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
if ( read.getReadUnmappedFlag() ) totalUnmappedReads++;
|
||||||
|
else {
|
||||||
|
// destroy mate pair mapping information, if any (we will need to reconstitute pairs after remapping both ends):
|
||||||
|
read.setMateReferenceIndex(SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX);
|
||||||
|
read.setMateAlignmentStart(SAMRecord.NO_ALIGNMENT_START);
|
||||||
|
// if ( read.getReadPairedFlag() ) System.out.println("PAIRED READ!!");
|
||||||
|
}
|
||||||
|
totalRecords++;
|
||||||
|
|
||||||
|
if ( totalRecords % 1000000 == 0 ) System.out.println(totalRecords + " valid records processed");
|
||||||
|
|
||||||
|
|
||||||
|
if ( ! read.getReadName().equals(lastReadName) ) {
|
||||||
|
totalReads++;
|
||||||
|
lastReadName = read.getReadName();
|
||||||
|
|
||||||
|
|
||||||
|
if ( REDUCE ) {
|
||||||
|
for ( SAMRecord r : remappedReads ) {
|
||||||
|
writer.addAlignment(r); // emit non-redundant alignments for previous query
|
||||||
|
writtenRecords++;
|
||||||
|
}
|
||||||
|
remappedReads.clear();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if ( REDUCE ) remappedReads.add(read);
|
||||||
|
else {
|
||||||
|
writer.addAlignment(read);
|
||||||
|
writtenRecords++;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// write remaining bunch of reads:
|
||||||
|
if ( REDUCE ) {
|
||||||
|
for ( SAMRecord r : remappedReads ) {
|
||||||
|
writer.addAlignment(r); // emit non-redundant alignments for previous query
|
||||||
|
writtenRecords++;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
System.out.println("Total valid records processed: "+totalRecords);
|
||||||
|
System.out.println("Incorrect records (alignments across contig boundary) detected: "+badRecords +
|
||||||
|
" (discarded and excluded from any other stats)");
|
||||||
|
System.out.println("Total reads processed: "+totalReads);
|
||||||
|
System.out.println("Total mapped reads: "+(totalReads-totalUnmappedReads));
|
||||||
|
System.out.println("Average hits per mapped read: "+((double)(totalRecords-totalUnmappedReads))/(totalReads-totalUnmappedReads));
|
||||||
|
System.out.println("Records written: "+writtenRecords);
|
||||||
|
System.out.println("Average hits per mapped read written (after reduction): "
|
||||||
|
+((double)(writtenRecords-totalUnmappedReads))/(totalReads-totalUnmappedReads));
|
||||||
|
reader.close();
|
||||||
|
writer.close();
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
class AlignmentComparator implements Comparator<SAMRecord> {
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public int compare(SAMRecord r1, SAMRecord r2) {
|
||||||
|
// TODO Auto-generated method stub
|
||||||
|
if ( r1.getReferenceIndex() < r2.getReferenceIndex() ) return -1;
|
||||||
|
if ( r1.getReferenceIndex() > r2.getReferenceIndex() ) return 1;
|
||||||
|
if ( r1.getAlignmentStart() < r2.getAlignmentStart() ) return -1;
|
||||||
|
if ( r1.getAlignmentStart() > r2.getAlignmentStart() ) return 1;
|
||||||
|
return r1.getCigarString().compareTo(r2.getCigarString());
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
Loading…
Reference in New Issue