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Use results from SBI index instead of ignoring them #124

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Merged
merged 2 commits into from
Dec 12, 2019
Merged

Use results from SBI index instead of ignoring them #124

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bbf695a
Use results from SBI index instead of ignoring them
lbergelson Dec 5, 2019
c9b2df7
fix formatting
lbergelson Dec 5, 2019
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40 changes: 20 additions & 20 deletions src/main/java/org/disq_bio/disq/impl/formats/bam/BamSource.java
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Original file line number Diff line number Diff line change
Expand Up @@ -102,7 +102,7 @@ protected JavaRDD<PathChunk> getPathChunks(
try (SeekableStream sbiStream = fileSystemWrapper.open(jsc.hadoopConfiguration(), sbiPath)) {
SBIIndex sbiIndex = SBIIndex.load(sbiStream);
Broadcast<SBIIndex> sbiIndexBroadcast = jsc.broadcast(sbiIndex);
pathSplitSource
return pathSplitSource
.getPathSplits(jsc, path, splitSize)
.flatMap(
pathSplit -> {
Expand All @@ -117,26 +117,26 @@ protected JavaRDD<PathChunk> getPathChunks(
}
});
}
} else {
logger.debug("Using guessing for finding splits");
SerializableHadoopConfiguration confSer =
new SerializableHadoopConfiguration(jsc.hadoopConfiguration());
return bgzfBlockSource
.getBgzfBlocks(jsc, path, splitSize)
.mapPartitionsWithIndex(
(Function2<Integer, Iterator<BgzfBlockGuesser.BgzfBlock>, Iterator<PathChunk>>)
(partitionIndex, bgzfBlocks) -> {
Configuration conf = confSer.getConf();
PathChunk pathChunk =
getFirstReadInPartition(conf, bgzfBlocks, stringency, referenceSourcePath);
logger.debug("PathChunk for partition {}: {}", partitionIndex, pathChunk);
if (pathChunk == null) {
return Collections.emptyIterator();
}
return Collections.singleton(pathChunk).iterator();
},
true);
}

logger.debug("Using guessing for finding splits");
SerializableHadoopConfiguration confSer =
new SerializableHadoopConfiguration(jsc.hadoopConfiguration());
return bgzfBlockSource
.getBgzfBlocks(jsc, path, splitSize)
.mapPartitionsWithIndex(
(Function2<Integer, Iterator<BgzfBlockGuesser.BgzfBlock>, Iterator<PathChunk>>)
(partitionIndex, bgzfBlocks) -> {
Configuration conf = confSer.getConf();
PathChunk pathChunk =
getFirstReadInPartition(conf, bgzfBlocks, stringency, referenceSourcePath);
logger.debug("PathChunk for partition {}: {}", partitionIndex, pathChunk);
if (pathChunk == null) {
return Collections.emptyIterator();
}
return Collections.singleton(pathChunk).iterator();
},
true);
}

/**
Expand Down