protected void splitNTrim(
Context context, String region, GATKTools gatk, String input, String output)
throws InterruptedException {
Logger.DEBUG("run SplitNCigarReads");
context.setStatus("run SplitNCigarReads");
context.getCounter(HalvadeCounters.TOOLS_GATK).increment(1);
gatk.runSplitNCigarReads(input, output, ref, region, newMaxQualScore);
HalvadeFileUtils.removeLocalFile(keep, input, context, HalvadeCounters.FOUT_GATK_TMP);
HalvadeFileUtils.removeLocalFile(keep, input.replaceAll(".bam", ".bai"));
}
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);
}
}
}
protected void elPrepPreprocess(
Context context, PreprocessingTools tools, SAMRecordIterator input, String output)
throws InterruptedException, IOException, QualityException, URISyntaxException {
String dictF = ref.substring(0, ref.lastIndexOf('.')) + ".dict";
String rg = createReadGroupRecordString(RGID, RGLB, RGPL, RGPU, RGSM);
String preSamOut = tmpFileBase + "-p1.sam";
String samOut = tmpFileBase + "-p2.sam";
String fCounts = tmpFileBase + "-features.count";
outHeader = header.clone();
outHeader.setSortOrder(SAMFileHeader.SortOrder.coordinate);
Logger.DEBUG("call elPrep");
context.setStatus("call elPrep");
int reads;
if (keep) {
reads =
tools.callElPrep(
preSamOut, samOut, inputIsBam ? null : rg, threads, input, outHeader, dictF);
} else {
reads =
tools.streamElPrep(
context, samOut, inputIsBam ? null : rg, threads, input, outHeader, dictF);
}
Logger.DEBUG(reads + " reads processed in elPrep");
context.getCounter(HalvadeCounters.IN_PREP_READS).increment(reads);
if (gff != null) {
Logger.DEBUG("featureCounts");
context.setStatus("featureCounts");
tools.runFeatureCounts(gff, samOut, fCounts, threads);
HalvadeFileUtils.uploadFileToHDFS(
context,
FileSystem.get(new URI(outputdir), context.getConfiguration()),
fCounts,
outputdir + context.getTaskAttemptID().toString() + ".count");
}
context.setStatus("convert SAM to BAM");
Logger.DEBUG("convert SAM to BAM");
tools.callSAMToBAM(samOut, output, threads);
context.setStatus("build bam index");
Logger.DEBUG("build bam index");
tools.runBuildBamIndex(output);
// remove temporary files
HalvadeFileUtils.removeLocalFile(keep, preSamOut, context, HalvadeCounters.FOUT_GATK_TMP);
HalvadeFileUtils.removeLocalFile(keep, samOut, context, HalvadeCounters.FOUT_GATK_TMP);
HalvadeFileUtils.removeLocalFile(keep, fCounts);
}
protected void RnaVariantCalling(
Context context, String region, GATKTools gatk, String input, String output)
throws InterruptedException {
// choose between unifiendgenotyper vs haplotypegenotyper
Logger.DEBUG("run variantCaller");
context.setStatus("run variantCaller");
context.getCounter(HalvadeCounters.TOOLS_GATK).increment(1);
gatk.runHaplotypeCaller(input, output, true, scc, sec, ref, null, region);
context.setStatus("cleanup");
context.getCounter(HalvadeCounters.OUT_VCF_FILES).increment(1);
HalvadeFileUtils.removeLocalFile(keep, input, context, HalvadeCounters.FOUT_GATK_TMP);
HalvadeFileUtils.removeLocalFile(keep, input.replaceAll(".bam", ".bai"));
}
protected String makeRegionFile(
Context context, ChromosomeRange r, PreprocessingTools tools, String region)
throws URISyntaxException, IOException, InterruptedException {
// if exome dont do but for exome filter on exomeBedFile
if (filterBedFile == null) {
r.writeToPicardRegionFile(region);
} else {
String exomebed = tmpFileBase + "exome.bed";
if (filterBedFile.endsWith(".gz")) {
exomebed += ".gz";
}
HalvadeFileUtils.downloadFileFromHDFS(
context,
FileSystem.get(new URI(filterBedFile), context.getConfiguration()),
filterBedFile,
exomebed);
if (exomebed.endsWith(".gz")) {
exomebed = HalvadeFileUtils.Unzip(exomebed);
}
region = tools.filterExomeBed(exomebed, r);
if (region == null) {
Logger.DEBUG("empty region file, no vcf results!!");
return null;
}
HalvadeFileUtils.removeLocalFile(keep, exomebed);
}
return region;
}
protected void annotateVariants(
Context context, String region, GATKTools gatk, String input, String output)
throws InterruptedException {
Logger.DEBUG("run VariantAnnotator");
context.setStatus("run VariantAnnotator");
context.getCounter(HalvadeCounters.TOOLS_GATK).increment(1);
gatk.runVariantAnnotator(input, output, ref, region);
HalvadeFileUtils.removeLocalFile(keep, input, context, HalvadeCounters.FOUT_GATK_TMP);
}
// TODO improve annotate/filter
protected void filterVariants(
Context context, String region, GATKTools gatk, String input, String output)
throws InterruptedException {
Logger.DEBUG("run VariantFiltration");
context.setStatus("run VariantFiltration");
context.getCounter(HalvadeCounters.TOOLS_GATK).increment(1);
gatk.runVariantFiltration(input, output, ref, region, windows, cluster, minFS, maxQD);
HalvadeFileUtils.removeLocalFile(keep, input, context, HalvadeCounters.FOUT_GATK_TMP);
}
protected void indelRealignment(
Context context, String region, GATKTools gatk, String input, String output)
throws InterruptedException {
String targets = tmpFileBase + ".intervals";
Logger.DEBUG("run RealignerTargetCreator");
context.setStatus("run RealignerTargetCreator");
context.getCounter(HalvadeCounters.TOOLS_GATK).increment(1);
gatk.runRealignerTargetCreator(input, targets, ref, region);
Logger.DEBUG("run IndelRealigner");
context.setStatus("run IndelRealigner");
context.getCounter(HalvadeCounters.TOOLS_GATK).increment(1);
gatk.runIndelRealigner(input, targets, output, ref, region);
HalvadeFileUtils.removeLocalFile(keep, input, context, HalvadeCounters.FOUT_GATK_TMP);
HalvadeFileUtils.removeLocalFile(keep, input.replaceAll(".bam", ".bai"));
HalvadeFileUtils.removeLocalFile(keep, targets, context, HalvadeCounters.FOUT_GATK_TMP);
}
@Override
public void closeAligner() throws InterruptedException {
// close last BWA aln
closeBWAAln();
// but now start sampe/samse
startBWASamXe();
ssh.join();
int error = samxe.waitForCompletion();
if (error != 0) throw new ProcessException("BWA samXe", error);
context.getCounter(HalvadeCounters.TIME_BWA_SAMPE).increment(samxe.getExecutionTime());
// remove all temporary fastq/sai files
HalvadeFileUtils.removeLocalFile(
keep, getFileName(tmpdir, taskId, true, 1), context, HalvadeCounters.FOUT_BWA_TMP);
HalvadeFileUtils.removeLocalFile(
keep, getFileName(tmpdir, taskId, false, 1), context, HalvadeCounters.FOUT_BWA_TMP);
HalvadeFileUtils.removeLocalFile(
keep, getFileName(tmpdir, taskId, true, 2), context, HalvadeCounters.FOUT_BWA_TMP);
HalvadeFileUtils.removeLocalFile(
keep, getFileName(tmpdir, taskId, false, 2), context, HalvadeCounters.FOUT_BWA_TMP);
instance = null;
}
protected void PicardPreprocess(
Context context, PreprocessingTools tools, SAMRecordIterator input, String output)
throws InterruptedException, QualityException, IOException, URISyntaxException {
outHeader = header.clone();
outHeader.setSortOrder(SAMFileHeader.SortOrder.coordinate);
// tmp files
String tmpOut1 = tmpFileBase + "-p1.bam";
String tmpOut2 = tmpFileBase + "-p2.bam";
String tmpOut3 = tmpFileBase + "-p3.sam";
String fCounts = tmpFileBase + "-features.count";
String tmpMetrics = tmpFileBase + "-p3-metrics.txt";
SAMFileWriterFactory factory = new SAMFileWriterFactory();
if (!inputIsBam) {
outHeader.addReadGroup(bamrg);
}
SAMFileWriter writer = factory.makeBAMWriter(outHeader, true, new File(tmpOut1));
long startTime = System.currentTimeMillis();
int count = 0;
SAMRecord sam;
while (input.hasNext()) {
sam = input.next();
writer.addAlignment(sam);
count++;
}
int reads = input.getCount();
writer.close();
context.getCounter(HalvadeCounters.IN_PREP_READS).increment(reads);
long estimatedTime = System.currentTimeMillis() - startTime;
context.getCounter(HalvadeCounters.TIME_HADOOP_SAMTOBAM).increment(estimatedTime);
Logger.DEBUG("time writing " + count + " records to disk: " + estimatedTime / 1000);
Logger.DEBUG("clean sam");
context.setStatus("clean sam");
tools.runCleanSam(tmpOut1, tmpOut2);
Logger.DEBUG("mark duplicates");
context.setStatus("mark duplicates");
tools.runMarkDuplicates(tmpOut2, tmpOut3, tmpMetrics);
if (gff != null) {
// tmpOut3 is sam for htseq count!
Logger.DEBUG("featureCounts");
context.setStatus("featureCounts");
tools.runFeatureCounts(gff, tmpOut3, fCounts, threads);
HalvadeFileUtils.uploadFileToHDFS(
context,
FileSystem.get(new URI(outputdir), context.getConfiguration()),
fCounts,
outputdir + context.getTaskAttemptID().toString() + ".count");
}
if (!inputIsBam) {
Logger.DEBUG("add read-group");
context.setStatus("add read-group");
tools.runAddOrReplaceReadGroups(tmpOut3, output, RGID, RGLB, RGPL, RGPU, RGSM);
} else {
context.setStatus("convert SAM to BAM");
Logger.DEBUG("convert SAM to BAM");
tools.callSAMToBAM(tmpOut3, output, threads);
}
Logger.DEBUG("build bam index");
context.setStatus("build bam index");
tools.runBuildBamIndex(output);
estimatedTime = System.currentTimeMillis() - startTime;
Logger.DEBUG("estimated time: " + estimatedTime / 1000);
// remove all temporary files now!
HalvadeFileUtils.removeLocalFile(keep, tmpMetrics, context, HalvadeCounters.FOUT_GATK_TMP);
HalvadeFileUtils.removeLocalFile(keep, tmpOut1, context, HalvadeCounters.FOUT_GATK_TMP);
HalvadeFileUtils.removeLocalFile(keep, tmpOut2, context, HalvadeCounters.FOUT_GATK_TMP);
HalvadeFileUtils.removeLocalFile(keep, tmpOut3, context, HalvadeCounters.FOUT_GATK_TMP);
HalvadeFileUtils.removeLocalFile(keep, fCounts);
}