protected void baseQualityScoreRecalibration(
Context context,
String region,
ChromosomeRange r,
PreprocessingTools tools,
GATKTools gatk,
String input,
String output)
throws InterruptedException, IOException, URISyntaxException {
String table = tmpFileBase + ".table";
// get snp database(s)
String[] snpslocal = HalvadeFileUtils.downloadSites(context, taskId);
String[] newKnownSites = new String[snpslocal.length];
for (int i = 0; i < snpslocal.length; i++) {
if (filterDBsnp) {
newKnownSites[i] =
tools.filterDBSnps(
ref.replaceAll("fasta", "dict"), snpslocal[i], r, tmpFileBase, threads);
} else {
newKnownSites[i] = snpslocal[i];
}
if (newKnownSites[i].endsWith(".gz")) {
newKnownSites[i] = HalvadeFileUtils.Unzip(newKnownSites[i]);
}
}
// should be created automatically by GATK v3.0 or higher
// Logger.DEBUG("build bam index");
// context.setStatus("build bam index");
// tools.runBuildBamIndex(tmpFile1);
Logger.DEBUG("run baseRecalibrator");
context.setStatus("run baseRecalibrator");
context.getCounter(HalvadeCounters.TOOLS_GATK).increment(1);
gatk.runBaseRecalibrator(input, table, ref, newKnownSites, region);
Logger.DEBUG("run printReads");
context.setStatus("run printReads");
context.getCounter(HalvadeCounters.TOOLS_GATK).increment(1);
gatk.runPrintReads(input, output, ref, table, region);
HalvadeFileUtils.removeLocalFile(keep, input, context, HalvadeCounters.FOUT_GATK_TMP);
HalvadeFileUtils.removeLocalFile(keep, input.replaceAll(".bam", ".bai"));
HalvadeFileUtils.removeLocalFile(keep, table, context, HalvadeCounters.FOUT_GATK_TMP);
for (int i = 0; i < newKnownSites.length; i++) {
if (filterDBsnp) {
HalvadeFileUtils.removeLocalFile(
keep, newKnownSites[i], context, HalvadeCounters.FOUT_GATK_TMP);
}
}
}
