Add a tool to make IGV-compat. BEDPE files from AggregateSvPileup #37
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clintval
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Apr 10, 2024
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| class _All extends ClpGroup { | ||
| override val name: String = "All tools" | ||
| override val description: String = "All tools." | ||
| class _BreakpointAndSv extends ClpGroup { | ||
| override val name: String = "Breakpoint and SV Tools" | ||
| override val description: String = "Primary tools for calling and transforming breakpoints and SVs." | ||
| } | ||
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| final val All = classOf[_All] | ||
| class _Utilities extends ClpGroup { | ||
| override val name: String = "Utility Tools" | ||
| override val description: String = "Helper tools for working with breakpoint or SV data." | ||
| } | ||
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| final val BreakpointAndSv = classOf[_BreakpointAndSv] | ||
| final val Utilities = classOf[_Utilities] |
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This is a backwards compatible change and make the CLI look like:
clintval
commented
Apr 10, 2024
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| end1 = pileup.left_max_pos + 1, | ||
| chrom2 = pileup.right_contig, | ||
| start2 = pileup.right_min_pos, | ||
| end2 = pileup.right_max_pos + 1, |
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Max positions are 0-based so to make them half-open we need to add 1.
EDIT: This was wrong! See #40
nh13
approved these changes
Apr 10, 2024
src/main/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileupToBedPE.scala
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src/main/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileupToBedPE.scala
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src/main/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileupToBedPE.scala
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Hopefully this addition is welcome! Converting the output of AggregateSvPileup to BEDPE facilitates genome-browsing in IGV and helps with understanding how breakpoint events relate to the alignments that cause them. There exist more advanced features of BEDPE in IGV (like record-specific coloring) but I chose not to implement that at this time to keep the tool simple and forwards compatible. Here is what test data looks like in IGV: