Trim intervals loaded from interval files. #6375
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lbergelson
requested changes
Jan 14, 2020
| ret.add(glParser.parseGenomeLoc(line)); | ||
| final String trimmedLine = line.trim(); | ||
| if (!trimmedLine.isEmpty()) { | ||
| ret.add(glParser.parseGenomeLoc(trimmedLine)); |
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There is at least one other call to parseGenomeLoc that are still not trimmed. See line 332. I think it should also be trimmed or the trimming should just be pushed down into parseGenomeLoc as well to be sure that it always happens.
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Added trim call to GenomeParserLoc, with a test.
| @Test | ||
| public void testIntervalFileIntervalsAreTrimmed() throws Exception { | ||
| final GenomeLoc expectedGenomeLoc = hg19GenomeLocParser.createGenomeLoc("1", 1, 10); | ||
| final File gatkIntervalFile = createTempFile("testIntervalFileIntervalsAreTrimmed", ".intervals.list", |
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Huh, I've never seen this method which creates the temp file and writes to it before. That seems useful. Maybe it should be promote somewhere.
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I moved it to IOUtils with other methods with similar functionality, though now its no longer test-only.
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Back to you @lbergelson . |
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Fixes #6371.