Support RepeatMasker output format for CHM13 (hs1) #15
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Adding repeats track fails: #16 |
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Adding CpG track fails: #17 |
| @@ -645,6 +645,7 @@ fun String.toStrand() = single().toStrand() | |||
| fun Char.toStrand() = when (this) { | |||
| '+' -> Strand.PLUS | |||
| '-' -> Strand.MINUS | |||
| 'C' -> Strand.MINUS | |||
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Can you please remove this option or add this super specific hs1 option processing to hs1 parsing?
Another possible solution is to add explicit comments on why we need this exception.
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I've moved this option to AnnotationsHs1.kt
| @@ -103,6 +119,67 @@ object Repeats { | |||
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| return builder.build() | |||
| } | |||
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| private fun parseHs1( | |||
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It would be better to add this code to the AnnotationsHs1.kt file and delegate it to specialized functions from this file. It will make adding the next extraordinary genome easier.
| return line.isNotBlank() && line.contains(chrMarker) && !line.contains(substringPresentOnlyInHeader) | ||
| } | ||
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| private fun parseHs1RepeatsLine(line: String, chromosomes: Map<String, Chromosome>): Pair<Chromosome, Repeat>? { |
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Please add a test with a short prepared test data for repeats in hs1 specific format.
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I've added some tests for hs1 repeats parsing.
* Support RepeatMasker output format for CHM13 (hs1) * Move methods related to hs1 repeats parsing to AnnotationsHs1.kt. * Added tests --------- Co-authored-by: Sergey Pestrikov <[email protected]>
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