Ignore specified contigs for pre-aligned BAMs in PathSeq #6537
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ldgauthier
approved these changes
Apr 15, 2020
| final Set<String> contigsToIgnoreSet = new HashSet<>(filterArgs.alignmentContigsToIgnore); | ||
| for (final String contig : contigsToIgnoreSet) { | ||
| if (dictionary.getSequence(contig) == null) { | ||
| throw new UserException.MissingContigInSequenceDictionary(contig, dictionary); |
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I'd like for the error to specify somehow is that the problem is the contigs specified for filtering. Otherwise users will be validating all their input files and scratching their heads.
| @@ -190,6 +193,16 @@ | |||
| optional = true) | |||
| public int minIdentity = 30; | |||
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| /** | |||
| * If using --is-host-aligned, ignores alignments to these contigs (can be specified multiple times). This | |||
| * can be useful if the alignment is to a reference containing a microbe, such as chrEBV in hg38. | |||
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Is it really called chrEBV? Honestly I haven't looked at all 3500 names.
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Yep. I recently found out it's also in hg19 but it uses the NCBI accession
| readA.setAttribute("NM", 0); | ||
| readA.setPosition(IGNORED_CONTIG, 1); | ||
| final boolean testA = filter.test(readA); | ||
| Assert.assertEquals(true, testA); |
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I prefer Assert.assertTrue and Assert.assertFalse (below)
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Adds an argument to PathSeq filtering that lets users specify any contigs that should be ignored. This is useful for BAMs aligned to hg38, which contains the Epstein-Barr virus (chrEBV).