Allowed > 2^31 hits

[rsem.git] / BamWriter.h

diff --git a/BamWriter.h b/BamWriter.h
index 12ab087d668966f905a495f4e608a777e157ebc0..a73e3da4dc180668b2ffac4845172ed061bf11c0 100644 (file)
--- a/BamWriter.h
+++ b/BamWriter.h
@@ -7,6 +7,7 @@
 #include<cassert>
 #include<string>
 #include<sstream>
+#include<iostream>
 
 #include <stdint.h>
 #include "sam/bam.h"
@@ -14,6 +15,8 @@
 #include "sam_rsem_aux.h"
 #include "sam_rsem_cvt.h"
 
+#include "utils.h"
+
 #include "SingleHit.h"
 #include "PairedEndHit.h"
 
@@ -76,13 +79,13 @@ void BamWriter::work(HitWrapper<SingleHit> wrapper) {
        bam1_t *b;
        SingleHit *hit;
 
-       int cnt = 0;
+       HIT_INT_TYPE cnt = 0;
 
        b = bam_init1();
 
        while (samread(in, b) >= 0) {
                ++cnt;
-               if (verbose && cnt % 1000000 == 0) { printf("%d alignment lines are loaded!\n", cnt); }
+               if (verbose && cnt % 1000000 == 0) { std::cout<< cnt<< "alignment lines are loaded!"<< std::endl; }
 
                if (b->core.flag & 0x0004) continue;
 
@@ -97,7 +100,7 @@ void BamWriter::work(HitWrapper<SingleHit> wrapper) {
        assert(wrapper.getNextHit() == NULL);
 
        bam_destroy1(b);
-       if (verbose) { printf("Bam output file is generated!\n"); }
+       if (verbose) { std::cout<< "Bam output file is generated!"<< std::endl; }
 }
 
 void BamWriter::work(HitWrapper<PairedEndHit> wrapper) {
@@ -111,8 +114,7 @@ void BamWriter::work(HitWrapper<PairedEndHit> wrapper) {
 
        while (samread(in, b) >= 0 && samread(in, b2) >= 0) {
                cnt += 2;
-               if (verbose && cnt % 1000000 == 0) { printf("%d alignment lines are loaded!\n", cnt); }
-
+               if (verbose && cnt % 1000000 == 0) { std::cout<< cnt<< "alignment lines are loaded!"<< std::endl; }
                //mate info is not complete, skip
                if (!(((b->core.flag & 0x0040) && (b2->core.flag & 0x0080)) || ((b->core.flag & 0x0080) && (b2->core.flag & 0x0040)))) continue;
                //unalignable reads, skip
@@ -148,7 +150,7 @@ void BamWriter::work(HitWrapper<PairedEndHit> wrapper) {
        bam_destroy1(b);
        bam_destroy1(b2);
 
-       if (verbose) { printf("Bam output file is generated!\n"); }
+       if (verbose) { std::cout<< "Bam output file is generated!"<< std::endl; }
 }
 
 void BamWriter::convert(bam1_t *b, double prb) {