Update addBedtoolsIntersect.R

fmalmeida · Sep 3, 2022 · 9f40bd9 · 9f40bd9
1 parent 12ee46a
commit 9f40bd9
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/bin/addBedtoolsIntersect.R b/bin/addBedtoolsIntersect.R
@@ -65,11 +65,11 @@ if (file.info(opt$txt)$size > 0) {
  colnames(bedtools_intersect) <- c("seqname1", "source1", "feature1", "start1", "end1", "score1", "strand1", "frame1", "attributes1",
  "seqname2", "source2", "feature2", "start2", "end2", "score2", "strand2", "frame2", "attributes2",
  "len")
- bedtools_intersect = bedtools_intersect[order(bedtools_intersect[,'attributes1'],-bedtools_intersect[,'len']),]
- bedtools_intersect = bedtools_intersect[!duplicated(bedtools_intersect$attributes1),]
 
  # Create a column in the intersection file with ids
  bedtools_intersect$ID <- getAttributeField(bedtools_intersect$attributes2, "ID", ";")
+ bedtools_intersect = bedtools_intersect[order(bedtools_intersect[,'ID'],-bedtools_intersect[,'len']),]
+ bedtools_intersect = bedtools_intersect[!duplicated(bedtools_intersect$ID),]
 
  # save ids
  ids <- bedtools_intersect$ID