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Better debug output for SAMDataSource 

output the name and number of the files being loaded by the GATK instead of "coordinate sorted".
This commit is contained in:
Mauricio Carneiro 2011-12-12 17:55:39 -05:00
parent 1ba1717ad8
commit a70a0f25fb
1 changed files with 3 additions and 2 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
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@ -711,6 +711,8 @@ public class SAMDataSource {
* @param validationStringency validation stringency. * @param validationStringency validation stringency.
*/ */
public SAMReaders(Collection<SAMReaderID> readerIDs, SAMFileReader.ValidationStringency validationStringency) { public SAMReaders(Collection<SAMReaderID> readerIDs, SAMFileReader.ValidationStringency validationStringency) {
int totalNumberOfFiles = readerIDs.size();
int readerNumber = 1;
for(SAMReaderID readerID: readerIDs) { for(SAMReaderID readerID: readerIDs) {
File indexFile = findIndexFile(readerID.samFile); File indexFile = findIndexFile(readerID.samFile);
@ -728,8 +730,7 @@ public class SAMDataSource {
reader.enableFileSource(true); reader.enableFileSource(true);
reader.setValidationStringency(validationStringency); reader.setValidationStringency(validationStringency);
final SAMFileHeader header = reader.getFileHeader(); logger.debug(String.format("Processing file (%d of %d) %s...", readerNumber++, totalNumberOfFiles, readerID.samFile));
logger.debug(String.format("Sort order is: " + header.getSortOrder()));
readers.put(readerID,reader); readers.put(readerID,reader);
} }