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modules/nextflow/src/main/groovy/nextflow/splitter Expand file tree Collapse file tree 1 file changed +8
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lines changed Original file line number Diff line number Diff line change @@ -134,14 +134,17 @@ class FastqSplitter extends AbstractTextSplitter {
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@Override
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protected fetchRecord (BufferedReader reader ) {
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- def l1 = reader. readLine()
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- def l2 = reader. readLine()
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- def l3 = reader. readLine()
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- def l4 = reader. readLine()
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+ final l1 = reader. readLine()
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+ final l2 = reader. readLine()
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+ final l3 = reader. readLine()
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+ final l4 = reader. readLine()
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- if ( ! l1 || ! l2 || ! l3 || ! l4 )
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+ if ( ! l1 && ! l2 && ! l3 && ! l4 )
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return null
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+ if ( ! l1 || ! l2 || ! l3 || ! l4 )
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+ throw new IllegalStateException (errorMessage)
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+
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if ( ! l1. startsWith(' @' ) || ! l3. startsWith(' +' ) )
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throw new IllegalStateException (errorMessage)
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