fd70c950c3e0f4c308bc3afd472a40fa98544d7b,src/test/java/org/seqdoop/hadoop_bam/TestBAMOutputFormat.java,TestBAMOutputFormat,testBAMRoundTrip,#,165

Before Change


        outputPath = doMapReduce(outFile.getAbsolutePath());

        // verify the final output
        blockStreamFile = new File(new File(outputPath.toUri()), "part-m-00000");
        final int actualCount = verifyBAMBlocks(
                blockStreamFile,
                samFileHeader,

After Change


        Path outputPath = doMapReduce(testBAMFileName);

        // merge the parts, and write to a temp file
        final File outFile = File.createTempFile("testBAMWriter", ".bam");
        outFile.deleteOnExit();
        SAMFileMerger.mergeParts(outputPath.toUri().toString(), outFile.toURI().toString(),
            SAMFormat.BAM, samFileHeader);

        // now use the assembled output as m/r input
        outputPath = doMapReduce(outFile.getAbsolutePath());

        // merge the parts again
        SAMFileMerger.mergeParts(outputPath.toUri().toString(), outFile.toURI().toString(),
            SAMFormat.BAM, samFileHeader);

        // verify the final output
        final int actualCount = getBAMRecordCount(outFile);