Renamed makefile as Makefile

[rsem.git] / bam2wig.cpp

diff --git a/bam2wig.cpp b/bam2wig.cpp
index b03d0b32e10eb8991f171dec1892a76a66fb9cd7..d205e8f7f4e9fde1cacef0ace99b626b18cc01d4 100644 (file)
--- a/bam2wig.cpp
+++ b/bam2wig.cpp
@@ -1,15 +1,25 @@
 #include <cstdio>
+#include <cstdlib>
+#include <cstring>
 
 #include "wiggle.h"
 
 using namespace std;
 
+void printUsage() {
+  printf("Usage: rsem-bam2wig sorted_bam_input wig_output wiggle_name [--no-fractional-weight]\n");
+  printf("sorted_bam_input\t: Input BAM format file, must be sorted\n");
+  printf("wig_output\t\t: Output wiggle file's name, e.g. output.wig\n");
+  printf("wiggle_name\t\t: the name of this wiggle plot\n");
+  printf("--no-fractional-weight\t: If this is set, RSEM will not look for \"ZW\" tag and each alignment appeared in the BAM file has weight 1. Set this if your BAM file is not generated by RSEM. Please note that this option must be at the end of the command line.\n");
+  exit(-1);
+}
+
 int main(int argc, char* argv[]) {
-       if (argc != 4) {
-               printf("Usage: rsem-bam2wig sorted_bam_input wig_output wiggle_name\n");
-               exit(-1);
-       }
+       if (argc < 4 || argc > 5) { printf("Number of arguments is not correct!\n"); printUsage(); }
+       if (argc == 5 && strcmp(argv[4], "--no-fractional-weight")) { printf("Cannot recognize option %s!\n", argv[4]); printUsage(); }
 
+       no_fractional_weight = (argc == 5 && !strcmp(argv[4], "--no-fractional-weight"));
        UCSCWiggleTrackWriter track_writer(argv[2], argv[3]);
        build_wiggles(argv[1], track_writer);