b56a73538d60ae3aa241b230d89b8b1ad74da5bd,core/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java,TraversalEngine,loadSAMFile,#File#boolean#,381
Before Change
samReader.setValidationStringency(strictness);
final SAMFileHeader header = samReader.getFileHeader();
System.err.println("Sort order is: " + header.getSortOrder());
// If the file has an index, querying functions are available. Use them if possible...
if (samReader.hasIndex()) {
After Change
samReader.setValidationStringency(strictness);
final SAMFileHeader header = samReader.getFileHeader();
logger.info(String.format("Sort order is: " + header.getSortOrder()));
// If the file has an index, querying functions are available. Use them if possible...
if (samReader.hasIndex()) {