fix bug that caused bed12 blocks from -split with BAMs having M,N,I,M…

… operations. Thx to @mbroad1
arq5x · Mar 9, 2024 · 6213eeb · 6213eeb
1 parent 705ccfd
commit 6213eeb
Showing 1 changed file with 10 additions and 4 deletions.
diff --git a/src/utils/BlockedIntervals/BlockedIntervals.cpp b/src/utils/BlockedIntervals/BlockedIntervals.cpp
@@ -41,8 +41,11 @@ void GetBamBlocks(const BamAlignment &bam,
                 if (!breakOnDeletionOps)
                     blockLength += cigItr->Length;
                 else {
-                    bedBlocks.push_back( BED(chrom, currPosition, currPosition + blockLength,
-                                          bam.Name, ToString(bam.MapQuality), strand) );
+                    if (blockLength > 0)
+                    {
+                        bedBlocks.push_back( BED(chrom, currPosition, currPosition + blockLength,
+                                            bam.Name, ToString(bam.MapQuality), strand) );
+                    }
                     currPosition += cigItr->Length + blockLength;
                     blockLength = 0;
                 }
@@ -51,8 +54,11 @@ void GetBamBlocks(const BamAlignment &bam,
                 if (!breakOnSkipOps)
                     blockLength += cigItr->Length;
                 else {
-                    bedBlocks.push_back( BED(chrom, currPosition, currPosition + blockLength,
-                                          bam.Name, ToString(bam.MapQuality), strand) );
+                    if (blockLength > 0)
+                    {
+                        bedBlocks.push_back( BED(chrom, currPosition, currPosition + blockLength,
+                                            bam.Name, ToString(bam.MapQuality), strand) );
+                    }
                     currPosition += cigItr->Length + blockLength;
                     blockLength = 0;
                 }