Correct bug where 1 would be erroneously added to sequence lengthts.

oist · Aug 5, 2024 · 0d59ed3 · 0d59ed3
1 parent 17c5d8f
commit 0d59ed3
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Showing 3 changed files with 6 additions and 5 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: GenomicBreaks
 Type: Package
 Title: Pairwise Alignment Breakpoint Analysis
-Version: 0.14.6
+Version: 0.14.7
 Authors@R: c(
   person("Charlotte", "West", email = "[email protected]", role = "aut"),
   person("Charles", "Plessy", email = "[email protected]",

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+# GenomicBreaks 0.14.7
+
+ * Correct a bug in `load_genomic_breaks()` where sequence lengths would be
+   too long of 1 nucleotide when loaded from MAF files.
+
 # GenomicBreaks 0.14.6
 
  * Experimental support for loading sequence information from FASTA files.

diff --git a/R/load_genomic_breaks.R b/R/load_genomic_breaks.R
@@ -133,14 +133,10 @@ load_genomic_breaks_MAF <- function (
   score(gb) <- l$scores
   seqlengths1        <- l $ seqlengths1 [!duplicated(l$seqnames1)]
   names(seqlengths1) <- l $ seqnames1   [!duplicated(l$seqnames1)]
-  # Add 1 to the lengths (see above)
-  seqlengths1 <- seqlengths1 + 1
   seqlengths(gb) <- seqlengths1
   gb$query <- GRanges(l$seqnames2, IRanges(l$start2, width = l$length2))
   seqlengths2        <- l $ seqlengths2 [!duplicated(l$seqnames2)]
   names(seqlengths2) <- l $ seqnames2   [!duplicated(l$seqnames2)]
-  # Add 1 to the lengths (see above)
-  seqlengths2 <- seqlengths2 + 1
   seqlengths(gb$query) <- seqlengths2
   gb$aLength <- l$aLength
   gb$matches <- l$matches