From a70a0f25fb9f7f791ab2b153e5c3d71cdcd1a21c Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Mon, 12 Dec 2011 17:55:39 -0500 Subject: [PATCH] Better debug output for SAMDataSource output the name and number of the files being loaded by the GATK instead of "coordinate sorted". --- .../sting/gatk/datasources/reads/SAMDataSource.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java index 2b163ecbd..d70c63bd2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java @@ -711,6 +711,8 @@ public class SAMDataSource { * @param validationStringency validation stringency. */ public SAMReaders(Collection readerIDs, SAMFileReader.ValidationStringency validationStringency) { + int totalNumberOfFiles = readerIDs.size(); + int readerNumber = 1; for(SAMReaderID readerID: readerIDs) { File indexFile = findIndexFile(readerID.samFile); @@ -728,8 +730,7 @@ public class SAMDataSource { reader.enableFileSource(true); reader.setValidationStringency(validationStringency); - final SAMFileHeader header = reader.getFileHeader(); - logger.debug(String.format("Sort order is: " + header.getSortOrder())); + logger.debug(String.format("Processing file (%d of %d) %s...", readerNumber++, totalNumberOfFiles, readerID.samFile)); readers.put(readerID,reader); }