add new files

[rsem.git] / tbam2gbam.cpp

diff --git a/tbam2gbam.cpp b/tbam2gbam.cpp
new file mode 100644 (file)
index 0000000..18688d0
--- /dev/null
+++ b/tbam2gbam.cpp
@@ -0,0 +1,31 @@
+#include<cstdio>
+#include<cstring>
+#include<cstdlib>
+
+#include "utils.h"
+#include "Transcripts.h"
+#include "BamConverter.h"
+
+using namespace std;
+
+char tiF[STRLEN], chr_list[STRLEN];
+Transcripts transcripts;
+
+int main(int argc, char* argv[]) {
+       if (argc != 4) {
+               printf("Usage: rsem-tbam2gbam reference_name unsorted_transcript_bam_input genome_bam_output\n");
+               exit(-1);
+       }
+
+       sprintf(tiF, "%s.ti", argv[1]);
+       sprintf(chr_list, "%s.chrlist", argv[1]);
+       transcripts.readFrom(tiF);
+
+       printf("Start converting:\n");
+       BamConverter bc(argv[2], argv[3], chr_list, transcripts);
+       bc.process();
+       printf("Genome bam file is generated!\n");
+
+       return 0;
+}
+