ACTIN-292: Add Chromosomal Rearrangements #612
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kduyvesteyn
approved these changes
Sep 19, 2024
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The logic looks good to me! Would be good to update the actual README at some point since you do make some assumptions (e.g. 98% deleted -> deletion).
Are you sure that in both cases the "far" arm is the Q arm in both chr1 and chr19? I will check with Charles, also just out of interest
...datamodel/src/main/java/com/hartwig/hmftools/datamodel/purple/ChromosomalRearrangements.java
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kduyvesteyn
approved these changes
Sep 19, 2024
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cbruel
commented
Sep 19, 2024
| { | ||
| int centromere1 = refGenomeCoordinates.centromere(CHR_1); | ||
| int centromere19 = refGenomeCoordinates.centromere(CHR_19); | ||
| int length19QArm = refGenomeCoordinates.length(CHR_19) - centromere19; |
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@kduyvesteyn Should there be a "+ 1" added here? Same in line 43.
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@kduyvesteyn I made some drawings and looked into how this is calculated in SvUtilities, and figured it out :)
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