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new optional arg added that allows to specify a separate bam file to send all piles that fail to realign to; plus minor fixes 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@691 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-05-13 20:24:23 +00:00
parent 8cce3d908f
commit de0cce87ea
2 changed files with 14 additions and 4 deletions
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11
java/src/org/broadinstitute/sting/playground/indels/IndelInspectorMain.java
View File

@ -24,14 +24,15 @@ public class IndelInspectorMain extends CommandLineProgram {
@Option(shortName="I", doc="SAM or BAM file for calling",optional=true) public File INPUT_FILE;
@Option(shortName="L",doc="Genomic interval to run on, as contig[:start[-stop]]; whole genome if not specified", optional=true) public String GENOME_LOCATION;
@Option(shortName="V",doc="Verbosity level: SILENT, PILESUMMARY, ALIGNMENTS", optional=true) public String VERBOSITY_LEVEL;
@Option(doc="Output file (sam or bam) for non-indel related reads and indel reads that were not improved") public String OUT1;
@Option(doc="Output file (sam or bam) for non-indel related reads and indel reads that were not improved (see OUTF)") public String OUT1;
@Option(doc="Output file (sam or bam) for improved (realigned) indel related reads") public String OUT2;
@Option(doc="Output file (sam or bam) for indel related reads that fail to realign", optional = true ) public String OUTF;
@Option(doc="[paranoid] If true, all reads that would be otherwise picked and processed by this tool will be saved, unmodified, into OUT1", optional=true) public Boolean CONTROL_RUN;
@Option(doc="Error counting mode: MM - mismatches only (from sam tags), MC - mismatches only doing actual mismatch count on the fly (use this if tags are incorrectly set); ERR - errors (arachne style: mm+gap lengths), MG - count mismatches and gaps as one error each") public String ERR_MODE;
@Option(doc="Maximum number of errors allowed (see ERR_MODE)") public Integer MAX_ERRS;
@Option(shortName="R", doc="Reference fasta or fasta.gz file") public File REF_FILE;
@Option(doc="Ignore reads that are longer than the specified cutoff (not a good way to do things but might be necessary because of performance issues)", optional=true) public Integer MAX_READ_LENGTH;
@Option(doc="Realignment will be attempted around trains of indels with at least of them observed COUNT_CUTOFF times or more",optional=true) public Integer COUNT_CUTOFF;
@Option(doc="Realignment will be attempted around trains of indels with at least one indel observed COUNT_CUTOFF times or more",optional=true) public Integer COUNT_CUTOFF;
/** Required main method implementation. */
public static void main(final String[] argv) {
@ -60,6 +61,8 @@ public class IndelInspectorMain extends CommandLineProgram {
location = GenomeLoc.parseGenomeLoc(GENOME_LOCATION);
}
if ( COUNT_CUTOFF == null ) COUNT_CUTOFF = 2;
if ( ! ERR_MODE.equals("MM") && ! ERR_MODE.equals("MG") && ! ERR_MODE.equals("ERR") && ! ERR_MODE.equals("MC") ) {
System.out.println("Unknown value specified for ERR_MODE: "+ERR_MODE);
return 1;
@ -77,9 +80,11 @@ public class IndelInspectorMain extends CommandLineProgram {
IndelRecordPileCollector col = null;
PassThroughWriter ptWriter = new PassThroughWriter(OUT1,samReader.getFileHeader());
PassThroughWriter ptFailedWriter = null;
if ( OUTF != null ) ptFailedWriter = new PassThroughWriter(OUTF,samReader.getFileHeader());
PileBuilder pileBuilder = null;
if ( CONTROL_RUN == null ) CONTROL_RUN=false;
if ( ! CONTROL_RUN ) pileBuilder = new PileBuilder(OUT2,samReader.getFileHeader(),ptWriter);
if ( ! CONTROL_RUN ) pileBuilder = new PileBuilder(OUT2,samReader.getFileHeader(), ptFailedWriter == null? ptWriter : ptFailedWriter);
try {
if ( CONTROL_RUN ) col = new IndelRecordPileCollector(ptWriter, new DiscardingPileReceiver() );

7
java/src/org/broadinstitute/sting/playground/indels/PileBuilder.java
View File

@ -357,11 +357,16 @@ public class PileBuilder implements RecordPileReceiver {
int id = id_iter.next();
SAMRecord r = as_list.get(id);
if ( pile_failed || pile_unmodified ) {
if ( pile_failed ) {
failedPileReceiver.receive(r); // nothing to do, send failed piles directly for writing
continue;
}
if ( pile_unmodified ) {
samWriter.addAlignment(r); // nothing to do, "cleaned" pile has not changed, so we just write all reads back
continue;
}
// we improved stuff!! let's reset the alignment parameters!
int cons_offset = ma.getOffsetWrtConsensus(id); // offset of the read 'id' wrt multiple alignment's full consensus seq