X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=parseIt.cpp;fp=parseIt.cpp;h=f40f82295302c48b16923d6655f3757d4057e09b;hp=91a4c141da95323dc58b5a8b45e47cb543fa0a75;hb=591e8c263863b1e024debc9944f8873080079503;hpb=f0f013a727d36ba4c63edfcee634b4aeef960750

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();