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[query] Fix data race in FASTA reader #9427

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merged 1 commit into from Sep 10, 2020
Merged

[query] Fix data race in FASTA reader #9427

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12 changes: 8 additions & 4 deletions hail/src/main/scala/is/hail/io/reference/FASTAReader.scala
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Expand Up @@ -73,7 +73,7 @@ class FASTAReader(val tmpdir: String, val fsBc: BroadcastValue[FS], val rg: Refe
reader.value.getSubsequenceAt(contig, start, if (end > maxEnd) maxEnd else end).getBaseString
}

private def fillBlock(blockIdx: Int) {
private def fillBlock(blockIdx: Int): String = {
val seq = new StringBuilder
val start = blockIdx.toLong * blockSize
var pos = start
Expand All @@ -85,13 +85,17 @@ class FASTAReader(val tmpdir: String, val fsBc: BroadcastValue[FS], val rg: Refe
pos += query.length
}

cache.put(blockIdx, seq.result())
val res = seq.result()
cache.put(blockIdx, res)
res
}

private def readBlock(blockIdx: Int): String = {
if (!cache.containsKey(blockIdx))
val x = cache.get(blockIdx)
if (x != null)
x
else
fillBlock(blockIdx)
cache.get(blockIdx)
}

private def readBlock(blockIdx: Int, offset: Int): String = {
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