break; // for 'H' - hard clip, do nothing to AlignedBases, move to next op\r
\r
default:\r
- printf("ERROR: Invalid Cigar op type\n"); // shouldn't get here\r
+ fprintf(stderr, "ERROR: Invalid Cigar op type\n"); // shouldn't get here\r
exit(1);\r
}\r
}\r
break;\r
\r
default : \r
- printf("ERROR: Invalid tag value type\n"); // shouldn't get here\r
+ fprintf(stderr, "ERROR: Invalid tag value type\n"); // shouldn't get here\r
exit(1);\r
}\r
}\r
// determine possible offsets\r
vector<int64_t> offsets;\r
if ( !NewIndex->GetOffsets(Region, IsRightBoundSpecified, offsets) ) {\r
- printf("ERROR: Could not jump: unable to calculate offset for specified region.\n");\r
+ fprintf(stderr, "ERROR: Could not jump: unable to calculate offset for specified region.\n");\r
return false;\r
}\r
\r
// check to see if proper BAM header\r
char buffer[4];\r
if (mBGZF.Read(buffer, 4) != 4) {\r
- printf("Could not read header type\n");\r
+ fprintf(stderr, "Could not read header type\n");\r
exit(1);\r
}\r
\r
if (strncmp(buffer, "BAM\001", 4)) {\r
- printf("wrong header type!\n");\r
+ fprintf(stderr, "wrong header type!\n");\r
exit(1);\r
}\r
\r