remove threshold for indel annotation
@@ -474,46 +474,26 @@ public class ConsequenceTypeGenericRegionCalculator extends ConsequenceTypeCalcu
}
if (regionsOverlap(spliceSite1, spliceSite1 + 1, variantStart, variantEnd)) { // Variant donor/acceptor
- if ((variantEnd - variantStart) <= BIG_VARIANT_SIZE_THRESHOLD) { // Big cnvs should not be annotated with such a detail
SoNames.add(leftSpliceSiteTag); // donor/acceptor depending on transcript strand
// BE CAREFUL: there are introns shorter than 7nts, and even just 1nt long!! (22:36587846)
junctionSolution[0] = (variantStart <= spliceSite2 || variantEnd <= spliceSite2);
- } else {
- // BE CAREFUL: there are introns shorter than 7nts, and even just 1nt long!! (22:36587846)
- junctionSolution[0] = (variantStart <= spliceSite2 || variantEnd <= spliceSite2);
- }
} else if (regionsOverlap(spliceSite1 + 2, spliceSite1 + 7, variantStart, variantEnd)) {
// Insertion coordinates are passed to this function as (variantStart-1,variantStart)
- if ((variantEnd - variantStart) <= BIG_VARIANT_SIZE_THRESHOLD) {
SoNames.add(VariantAnnotationUtils.SPLICE_REGION_VARIANT);
- }
// BE CAREFUL: there are introns shorter than 7nts, and even just 1nt long!! (22:36587846)
junctionSolution[0] = (variantStart <= spliceSite2 || variantEnd <= spliceSite2);
- } else if (regionsOverlap(spliceSite1 - 3, spliceSite1 - 1, variantStart, variantEnd)
- // Insertion coordinates are passed to this function as (variantStart-1,variantStart)
- && ((variantEnd - variantStart) <= BIG_VARIANT_SIZE_THRESHOLD)) {
+ } else if (regionsOverlap(spliceSite1 - 3, spliceSite1 - 1, variantStart, variantEnd)) {
SoNames.add(VariantAnnotationUtils.SPLICE_REGION_VARIANT);
}
if (regionsOverlap(spliceSite2 - 1, spliceSite2, variantStart, variantEnd)) { // Variant donor/acceptor
- if ((variantEnd - variantStart) <= BIG_VARIANT_SIZE_THRESHOLD) { // Big cnvs should not be annotated with such a detail
SoNames.add(rightSpliceSiteTag); // donor/acceptor depending on transcript strand
- // BE CAREFUL: there are introns shorter than 7nts, and even just 1nt long!! (22:36587846)
- junctionSolution[0] = (spliceSite1 <= variantStart || spliceSite1 <= variantEnd);
- } else {
- // BE CAREFUL: there are introns shorter than 7nts, and even just 1nt long!! (22:36587846)
junctionSolution[0] = (spliceSite1 <= variantStart || spliceSite1 <= variantEnd);
- }
} else if (regionsOverlap(spliceSite2 - 7, spliceSite2 - 2, variantStart, variantEnd)) {
- // Insertion coordinates are passed to this function as (variantStart-1,variantStart) {
- if ((variantEnd - variantStart) <= BIG_VARIANT_SIZE_THRESHOLD) {
SoNames.add(VariantAnnotationUtils.SPLICE_REGION_VARIANT);
- }
// BE CAREFUL: there are introns shorter than 7nts, and even just 1nt long!! (22:36587846)
junctionSolution[0] = (spliceSite1 <= variantStart || spliceSite1 <= variantEnd);
- } else if (regionsOverlap(spliceSite2 + 1, spliceSite2 + 3, variantStart, variantEnd)
- // Insertion coordinates are passed to this function as (variantStart-1,variantStart) {
- && ((variantEnd - variantStart) <= BIG_VARIANT_SIZE_THRESHOLD)) {
+ } else if (regionsOverlap(spliceSite2 + 1, spliceSite2 + 3, variantStart, variantEnd)) {
SoNames.add(VariantAnnotationUtils.SPLICE_REGION_VARIANT);
}
}
