/**
* Instantiates multiple underlying SAM writes, one per input SAM reader registered with GATK
* engine (those will be retrieved from <code>toolkit</code>). The output file names will be
* generated automatically by stripping ".sam" or ".bam" off the input file name and adding ext
* instead (e.g. ".cleaned.bam"). onto a unique output file name.
*
* @param toolkit
* @param ext
*/
public void setupByReader(
GenomeAnalysisEngine toolkit,
String ext,
SAMFileHeader.SortOrder order,
boolean presorted,
boolean indexOnTheFly,
boolean generateMD5,
SAMProgramRecord pRecord) {
for (SAMReaderID rid : toolkit.getReadsDataSource().getReaderIDs()) {
String fName = toolkit.getReadsDataSource().getSAMFile(rid).getName();
String outName;
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 + ext;
if (writerMap.containsKey(rid))
throw new StingException(
"nWayOut mode: Reader id for input sam file " + fName + " is already registered");
addWriter(rid, outName, order, presorted, indexOnTheFly, generateMD5, pRecord);
}
}
/**
* Instantiates multiple underlying SAM writes, one per input SAM reader registered with GATK
* engine (those will be retrieved from <code>toolkit</code>). The <code>in2out</code> map must
* contain an entry for each input filename and map it onto a unique output file name.
*
* @param toolkit
* @param in2out
*/
public void setupByReader(
GenomeAnalysisEngine toolkit,
Map<String, String> in2out,
SAMFileHeader.SortOrder order,
boolean presorted,
boolean indexOnTheFly,
boolean generateMD5,
SAMProgramRecord pRecord) {
if (in2out == null)
throw new StingException("input-output bam filename map for n-way-out writing is NULL");
for (SAMReaderID rid : toolkit.getReadsDataSource().getReaderIDs()) {
String fName = toolkit.getReadsDataSource().getSAMFile(rid).getName();
String outName;
if (!in2out.containsKey(fName))
throw new UserException.BadInput(
"Input-output bam filename map does not contain an entry for the input file " + fName);
outName = in2out.get(fName);
if (writerMap.containsKey(rid))
throw new StingException(
"nWayOut mode: Reader id for input sam file "
+ fName
+ " is already registered; "
+ "map file likely contains multiple entries for this input file");
addWriter(rid, outName, order, presorted, indexOnTheFly, generateMD5, pRecord);
}
}
public void addAlignment(SAMRecord samRecord) {
final SAMReaderID id = toolkit.getReaderIDForRead(samRecord);
String rg = samRecord.getStringAttribute("RG");
if (rg != null) {
String rg_orig = toolkit.getReadsDataSource().getOriginalReadGroupId(rg);
samRecord.setAttribute("RG", rg_orig);
}
addAlignment(samRecord, id);
}
