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Htsjdk Beta API first usage #1981

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Htsjdk Beta API first usage #1981

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7584853
refactoring overlap detector to use modern code before starting
lbergelson Nov 22, 2024
196e2df
Converting to use Beta API
lbergelson Nov 22, 2024
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49 changes: 33 additions & 16 deletions src/main/java/picard/sam/AddOATag.java
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,17 @@

package picard.sam;

import htsjdk.beta.codecs.reads.cram.CRAMDecoderOptions;
import htsjdk.beta.codecs.reads.cram.CRAMEncoderOptions;
import htsjdk.beta.exception.HtsjdkException;
import htsjdk.beta.plugin.reads.ReadsDecoder;
import htsjdk.beta.plugin.reads.ReadsDecoderOptions;
import htsjdk.beta.plugin.reads.ReadsEncoder;
import htsjdk.beta.plugin.reads.ReadsEncoderOptions;
import htsjdk.beta.plugin.registry.HtsCodecRegistry;
import htsjdk.beta.plugin.registry.HtsCodecResolver;
import htsjdk.beta.plugin.registry.HtsDefaultRegistry;
import htsjdk.io.IOPath;
import htsjdk.samtools.*;
import htsjdk.samtools.util.*;
import htsjdk.tribble.annotation.Strand;
Expand All @@ -34,8 +45,8 @@
import picard.cmdline.CommandLineProgram;
import picard.cmdline.StandardOptionDefinitions;
import picard.cmdline.programgroups.ReadDataManipulationProgramGroup;
import picard.nio.PicardHtsPath;

import java.io.File;
import java.io.IOException;
import java.util.List;
import java.util.Optional;
Expand All @@ -62,31 +73,39 @@ public class AddOATag extends CommandLineProgram {
"</pre>";

@Argument(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "SAM or BAM input file")
public String INPUT;
public PicardHtsPath INPUT;

@Argument(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc = "SAM or BAM file to write merged result to")
public String OUTPUT;
public PicardHtsPath OUTPUT;

@Argument(shortName = "L", doc = "If provided, only records that overlap given interval list will have the OA tag added.", optional = true)
public File INTERVAL_LIST;
public PicardHtsPath INTERVAL_LIST;

private static final Log log = Log.getInstance(AddOATag.class);

@Override
protected int doWork() {
try (final SamReader reader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(IOUtil.getPath(INPUT));
final SAMFileWriter writer = new SAMFileWriterFactory().makeWriter(reader.getFileHeader(), true, IOUtil.getPath(OUTPUT), REFERENCE_SEQUENCE)) {
writer.setProgressLogger(
new ProgressLogger(log, (int) 1e7, "Wrote", "records"));
ReadsDecoderOptions readsDecoderOptions = new ReadsDecoderOptions()
.setCRAMDecoderOptions(new CRAMDecoderOptions()
.setReferencePath(referenceSequence.getHtsPath()));
ReadsEncoderOptions readsEncoderOptions = new ReadsEncoderOptions()
.setPreSorted(true)
.setCRAMEncoderOptions(new CRAMEncoderOptions()
.setReferencePath(referenceSequence.getHtsPath()));

final OverlapDetector overlapDetector = getOverlapDetectorFromIntervalListFile(INTERVAL_LIST, 0, 0);
try (ReadsDecoder reader = HtsDefaultRegistry.getReadsResolver().getReadsDecoder(INPUT, readsDecoderOptions);
ReadsEncoder writer = HtsDefaultRegistry.getReadsResolver().getReadsEncoder(OUTPUT, readsEncoderOptions)) {
// unsupported writer.setProgressLogger(new ProgressLogger(log, (int) 1e7, "Wrote", "records"));
writer.setHeader(reader.getHeader());

final OverlapDetector<?> overlapDetector = getOverlapDetectorFromIntervalListFile(INTERVAL_LIST);
for (final SAMRecord rec : reader) {
if (overlapDetector == null || overlapDetector.overlapsAny(rec)) {
setOATag(rec);
}
writer.addAlignment(rec);
writer.write(rec);
}
} catch (IOException e) {
} catch (HtsjdkException e) {
log.error(e);
return 1;
}
Expand All @@ -95,14 +114,12 @@ protected int doWork() {
}

// Take an interval list file and convert it to an overlap detector, can add left and right padding
static OverlapDetector<Interval> getOverlapDetectorFromIntervalListFile(final File intervalList, final int lhsBuffer, final int rhsBuffer) {
static OverlapDetector<Interval> getOverlapDetectorFromIntervalListFile(final IOPath intervalList) {
if (intervalList == null) {
return null;
}
List<Interval> intervals = IntervalList.fromFile(intervalList).uniqued().getIntervals();
OverlapDetector<Interval> detector = new OverlapDetector<>(lhsBuffer, rhsBuffer);
detector.addAll(intervals, intervals);
return detector;
List<Interval> intervals = IntervalList.fromPath(intervalList.toPath()).uniqued().getIntervals();
return OverlapDetector.create(intervals);
}

// format OA tag string according to the spec
Expand Down
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