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()) {