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NWayOut logic slightly changed: 1) results.list file is gone; 2) now with -nWayOut one can specify either a) suffix to attach to every output file (i.e. cleaned reads from inputK.bam will be sent to inputK.suffix.bam) or b) *.map tab-separated file that must list <input_name> <output_name> mappings, one per line, for every input file. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4645 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-11-10 20:32:16 +00:00
parent a1adfb91ce
commit 2e0296fef9
1 changed files with 57 additions and 32 deletions
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89
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -48,6 +48,7 @@ import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator;
import org.broadinstitute.sting.utils.interval.NwayIntervalMergingIterator;
import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import org.broadinstitute.sting.utils.text.XReadLines;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.collections.Pair;
@ -55,6 +56,7 @@ import org.broadinstitute.sting.utils.collections.Pair;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.FileReader;
import java.util.*;
/**
@ -132,12 +134,14 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
@Hidden
@Argument(fullName="nWayOut", shortName="nWayOut", required=false,
doc="In this mode, there will be one output file for each input (-I) bam file. Reads from all input files "+
doc="Generate one output file for each input (-I) bam file. Reads from all input files "+
"will be realigned together, but then each read will be saved in the output file corresponding to "+
"the input file the read came from. The names of the output bam files will be constructed by "+
"stripping extensions (\".bam\" or \".sam\") from the input file names and pasting the value "+
"of -nWayOut argument to the result. The names of all output files will be also saved in a "+
"separate results.list file")
"the input file the read came from. There are two ways to generate output bam file names: 1) if the "+
"value of this argument is a general string (e.g. '.cleaned.bam'), then "+
"extensions (\".bam\" or \".sam\") will be stripped from the input file names and the provided string value "+
"will be pasted on instead; 2) if the value ends with a '.map' (e.g. input_output.map), then " +
"the two-column tab-separated file with the specified name must exist and list unique output file name (2nd column)" +
"for each input file name (1st column).")
protected String N_WAY_OUT = null;
@ -230,47 +234,68 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
if ( writer != null ) throw new UserException.BadInput("-nWayOut and -o arguments are mutually exclusive");
FileWriter fw;
try {
fw = new FileWriter("results.list");
} catch (IOException e) {
throw new StingException("I/O error: Failed to create results.list file");
nwayWriters = new HashMap<SAMReaderID,SAMFileWriter>();
Map<String,String> fname_map = null;
if ( N_WAY_OUT.toUpperCase().endsWith(".MAP") ) {
fname_map = new HashMap<String,String>();
try {
XReadLines reader = new XReadLines(new File(N_WAY_OUT),true);
for ( String line : reader ) {
if ( line.length() == 0 ) continue;
String fields[] = line.split("\t");
if ( fields.length != 2 )
throw new UserException.BadInput("Input-output map file must have exactly two columns. Offending line:\n"+line);
if ( fields[0].length() == 0 || fields[1].length() == 0 )
throw new UserException.BadInput("Input-output map file can not have empty strings in either column. Offending line:\n"+line);
if ( fname_map.containsKey(fields[0]) )
throw new UserException.BadInput("Input-output map file contains duplicate entries for input name "+fields[0]);
if ( fname_map.containsValue(fields[1]) )
throw new UserException.BadInput("Input-output map file maps multiple entries onto single output name "+fields[1]);
fname_map.put(fields[0],fields[1]);
}
} catch (IOException e) {
throw new StingException("I/O Error while reading input-output map file "+N_WAY_OUT+": "+e.getMessage());
}
}
nwayWriters = new HashMap<SAMReaderID,SAMFileWriter>();
SAMFileWriterImpl.setDefaultMaxRecordsInRam(MAX_RECORDS_IN_RAM);
for ( SAMReaderID rid : getToolkit().getReadsDataSource().getReaderIDs() ) {
String fName = getToolkit().getReadsDataSource().getSAMFile(rid).getName();
int pos ;
if ( fName.toUpperCase().endsWith(".BAM") ) pos = fName.toUpperCase().lastIndexOf(".BAM");
else {
if ( fName.toUpperCase().endsWith(".SAM") ) pos = fName.toUpperCase().lastIndexOf(".SAM");
else throw new UserException.BadInput("Input file name "+fName+" does not end with .sam or .bam");
String outName;
if ( fname_map != null ) {
if ( ! fname_map.containsKey(fName) )
throw new UserException.BadInput("Input-output map file does not contain an entry for the input file "+fName);
outName = fname_map.get(fName);
} else {
int pos ;
if ( fName.toUpperCase().endsWith(".BAM") ) pos = fName.toUpperCase().lastIndexOf(".BAM");
else {
if ( fName.toUpperCase().endsWith(".SAM") ) pos = fName.toUpperCase().lastIndexOf(".SAM");
else throw new UserException.BadInput("Input file name "+fName+" does not end with .sam or .bam");
}
String prefix = fName.substring(0,pos);
outName = prefix+N_WAY_OUT;
}
String prefix = fName.substring(0,pos);
if ( nwayWriters.containsKey( rid ) )
throw new StingException("nWayOut mode: Reader id for input sam file "+fName+" is already registered");
File f = new File(prefix+N_WAY_OUT);
SAMFileWriterImpl.setDefaultMaxRecordsInRam(MAX_RECORDS_IN_RAM);
File f = new File(outName);
SAMFileWriter sw = new SAMFileWriterFactory().makeSAMOrBAMWriter(setupHeader(getToolkit().getSAMFileHeader(rid)),
false,f);
try {
fw.append(f.getAbsolutePath());
fw.append('\n');
} catch (IOException e) {
throw new StingException("I/O error: write failed for results.list file"); //To change body of catch statement use File | Settings | File Templates.
}
nwayWriters.put(rid,sw);
}
try {
fw.close();
} catch (IOException e) {
throw new StingException("I/O error: failed to close results.list file"); //To change body of catch statement use File | Settings | File Templates.
}
}