Added error detection for cases such as a read's two mates having different names...

[rsem.git] / parseIt.cpp

diff --git a/parseIt.cpp b/parseIt.cpp
index 91a4c141da95323dc58b5a8b45e47cb543fa0a75..f40f82295302c48b16923d6655f3757d4057e09b 100644 (file)
--- 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();