X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2FBamReader.cpp;h=93a991bd77f942becb85fa505dba8b6334a15be1;hb=90bb3691f9aa2a2e8a4dd906c2439c7bc434eb78;hp=98ea7589f664de056f5138593e24454480bd26c7;hpb=1d03f81d725ffedeac9d9d73a2058f00cfc0b0e4;p=bamtools.git

diff --git a/src/api/BamReader.cpp b/src/api/BamReader.cpp
index 98ea758..93a991b 100644
--- a/src/api/BamReader.cpp
+++ b/src/api/BamReader.cpp
@@ -282,7 +282,7 @@ bool BamReader::BamReaderPrivate::BuildCharData(BamAlignment& bAlignment) {
                     break;  // for 'H' - hard clip, do nothing to AlignedBases, move to next op
                     
                 default:
-                    printf("ERROR: Invalid Cigar op type\n"); // shouldn't get here
+                    fprintf(stderr, "ERROR: Invalid Cigar op type\n"); // shouldn't get here
                     exit(1);
             }
         }
@@ -330,7 +330,7 @@ bool BamReader::BamReaderPrivate::BuildCharData(BamAlignment& bAlignment) {
                     break;
                 
                 default : 
-                    printf("ERROR: Invalid tag value type\n"); // shouldn't get here
+                    fprintf(stderr, "ERROR: Invalid tag value type\n"); // shouldn't get here
                     exit(1);
             }
         }
@@ -520,7 +520,7 @@ bool BamReader::BamReaderPrivate::Jump(int refID, int position) {
     // determine possible offsets
     vector<int64_t> offsets;
     if ( !NewIndex->GetOffsets(Region, IsRightBoundSpecified, offsets) ) {
-        printf("ERROR: Could not jump: unable to calculate offset for specified region.\n");
+        fprintf(stderr, "ERROR: Could not jump: unable to calculate offset for specified region.\n");
         return false;
     }
       
@@ -550,12 +550,12 @@ void BamReader::BamReaderPrivate::LoadHeaderData(void) {
     // check to see if proper BAM header
     char buffer[4];
     if (mBGZF.Read(buffer, 4) != 4) {
-        printf("Could not read header type\n");
+        fprintf(stderr, "Could not read header type\n");
         exit(1);
     }
 
     if (strncmp(buffer, "BAM\001", 4)) {
-        printf("wrong header type!\n");
+        fprintf(stderr, "wrong header type!\n");
         exit(1);
     }