X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parseIt.cpp;h=f40f82295302c48b16923d6655f3757d4057e09b;hb=b5ca7d97e07526eb3c66205e25fc643510a31fcf;hp=3373ef280979428230b74d77439d61bff3a96d47;hpb=509ffe2d71cf6a6f5cca8c39909f8ee10b8db899;p=rsem.git

diff --git a/parseIt.cpp b/parseIt.cpp
index 3373ef2..f40f822 100644
--- a/parseIt.cpp
+++ b/parseIt.cpp
@@ -52,7 +52,7 @@ void init(const char* imdName, char alignFType, const char* alignF) {
 
 	char* aux = 0;
 	if (strcmp(fn_list, "")) aux = fn_list;
-	parser = new SamParser(alignFType, alignF, transcripts, aux);
+	parser = new SamParser(alignFType, alignF, aux, transcripts, imdName);
 
 	memset(cat, 0, sizeof(cat));
 	memset(readOutFs, 0, sizeof(readOutFs));
@@ -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();