From fd7becfcdfd54bbf6f0c15461e8b525b10cec4f7 Mon Sep 17 00:00:00 2001
From: lindenb <plindenbaum@yahoo.fr>
Date: Tue, 22 Apr 2014 11:27:44 +0200
Subject: [PATCH] support for operators 'X' and '=' in method
BlockedIntervals.cpp/GetBamBlocks
---
src/utils/BlockedIntervals/BlockedIntervals.cpp | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/utils/BlockedIntervals/BlockedIntervals.cpp b/src/utils/BlockedIntervals/BlockedIntervals.cpp
index c653881e..ad88543b 100644
--- a/src/utils/BlockedIntervals/BlockedIntervals.cpp
+++ b/src/utils/BlockedIntervals/BlockedIntervals.cpp
@@ -33,7 +33,7 @@ void GetBamBlocks(const BamAlignment &bam,
vector<CigarOp>::const_iterator cigEnd = bam.CigarData.end();
for (; cigItr != cigEnd; ++cigItr) {
switch (cigItr->Type) {
- case ('M') :
+ case ('M') :case ('X'): case ('='):
blockLength += cigItr->Length;
case ('I') : break;
case ('S') : break;
@@ -58,7 +58,7 @@ void GetBamBlocks(const BamAlignment &bam,
}
case ('H') : break; // for 'H' - do nothing, move to next op
default :
- printf("ERROR: Invalid Cigar op type\n"); // shouldn't get here
+ fprintf(stderr,"ERROR: Invalid Cigar op type \'%c\'.\n",cigItr->Type); // shouldn't get here
exit(1);
}
}
@@ -119,4 +119,4 @@ int GetTotalBlockLength(const bedVector &bedBlocks) {
total_size += blockItr->end - blockItr->start;
}
return total_size;
-}
\ No newline at end of file
+}
--
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