Added .gitignore file back

[rsem.git] / scanForPairedEndReads.cpp

diff --git a/scanForPairedEndReads.cpp b/scanForPairedEndReads.cpp
index b220fa82f2dcd9d8c16843a9b18ac7f42611f06c..3669f5faad46972a6b2949a2226a6a159f284b67 100644 (file)
--- a/scanForPairedEndReads.cpp
+++ b/scanForPairedEndReads.cpp
@@ -50,7 +50,7 @@ bool less_than(bam1_t *a, bam1_t *b) {
 
 int main(int argc, char* argv[]) {
        if (argc != 3) {
-               printf("UsaOAge: rsem-scan-for-paired-end-reads input.sam output.bam\n");
+               printf("Usage: rsem-scan-for-paired-end-reads input.sam output.bam\n");
                exit(-1);
        }
 
@@ -75,12 +75,12 @@ int main(int argc, char* argv[]) {
                if (isPaired) {
                        add_to_appropriate_arr(b);
                        while ((go_on = (samread(in, b) >= 0)) && (qname == bam1_qname(b))) {
-                               general_assert(b->core.flag & 0x0001, "Read " + qname + " is detected as both single-end and paired-end read!", true);
+                               general_assert_1(b->core.flag & 0x0001, "Read " + qname + " is detected as both single-end and paired-end read!");
                                add_to_appropriate_arr(b);
                        }
 
-                       general_assert(arr_both.size() % 2 == 0, "Number of first and second mates in read " + qname + "'s full alignments (both mates are aligned) are not matched!", true);
-                       general_assert((arr_partial_1.size() + arr_partial_2.size() + arr_partial_unknown.size()) % 2 == 0, "Number of first and second mates in read " + qname + "'s partial alignments (at most one mate is aligned) are not matched!", true);
+                       general_assert_1(arr_both.size() % 2 == 0, "Number of first and second mates in read " + qname + "'s full alignments (both mates are aligned) are not matched!");
+                       general_assert_1((arr_partial_1.size() + arr_partial_2.size() + arr_partial_unknown.size()) % 2 == 0, "Number of first and second mates in read " + qname + "'s partial alignments (at most one mate is aligned) are not matched!");
 
                        if (!arr_both.empty()) {
                                sort(arr_both.begin(), arr_both.end(), less_than);