From 591e8c263863b1e024debc9944f8873080079503 Mon Sep 17 00:00:00 2001
From: Bo Li <bli@cs.wisc.edu>
Date: Wed, 3 Sep 2014 16:43:53 -0500
Subject: [PATCH] Added error detection for cases such as a read's two mates
having different names or a read is both alignable and unalignable
---
SamParser.h | 6 +++++-
parseIt.cpp | 3 +++
2 files changed, 8 insertions(+), 1 deletion(-)
diff --git a/SamParser.h b/SamParser.h
index 81d4097..4747ef4 100644
--- a/SamParser.h
+++ b/SamParser.h
@@ -62,7 +62,7 @@ private:
}
std::string getName(const bam1_t* b) {
- return std::string((char*)bam1_qname(b));
+ return std::string(bam1_qname(b));
}
std::string getReadSeq(const bam1_t*);
@@ -190,6 +190,8 @@ int SamParser::parseNext(PairedEndRead& read, PairedEndHit& hit) {
mp1 = b2; mp2 = b;
}
+ general_assert(!strcmp(bam1_qname(mp1), bam1_qname(mp2)), "Detected a read pair whose two mates have different names: " + getName(mp1) + " , " + getName(mp2) + " !");
+
int readType = getReadType(mp1, mp2);
std::string name = getName(mp1);
@@ -242,6 +244,8 @@ int SamParser::parseNext(PairedEndReadQ& read, PairedEndHit& hit) {
mp1 = b2; mp2 = b;
}
+ general_assert(!strcmp(bam1_qname(mp1), bam1_qname(mp2)), "Detected a read pair whose two mates have different names: " + getName(mp1) + " , " + getName(mp2) + " !");
+
int readType = getReadType(mp1, mp2);
std::string name = getName(mp1);
diff --git a/parseIt.cpp b/parseIt.cpp
index 91a4c14..f40f822 100644
--- a/parseIt.cpp
+++ b/parseIt.cpp
@@ -94,6 +94,9 @@ void parseIt(SamParser *parser) {
record_read.write(n_os, cat[record_val]);
++N[record_val];
}
+
+ general_assert(record_val == 1 || hits.getNHits() == 0, "Read " + record_read.getName() + " is both unalignable and alignable according to the input SAM/BAM file!");
+
// flush out previous read's hits if the read is alignable reads
if (record_val == 1) {
hits.updateRI();
--
2.39.5