Incoporated changes from Nils Homer.

[samtools.git] / bam_sort.c

diff --git a/bam_sort.c b/bam_sort.c
index abf8d4f6caf6dfeb25af423784934d78fe677478..e3a6c472cb1b50ddb0eab7273433a438c6dabede 100644 (file)
--- a/bam_sort.c
+++ b/bam_sort.c
@@ -418,6 +418,31 @@ void bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t m
        bam_sort_core_ext(is_by_qname, fn, prefix, max_mem, 0);
 }
 
+
+size_t bam_sort_get_max_mem(char *max_mem_string)
+{
+       char c;
+       size_t max_mem;
+       size_t multiplier=1;
+       c=max_mem_string[strlen(max_mem_string)-1];
+       switch(c) {
+       case 'G':
+               multiplier*=1024;
+       case 'M':
+               multiplier*=1024;
+       case 'K':
+               multiplier*=1024;
+       case 'B':
+               max_mem_string[strlen(max_mem_string)-1]='\0';
+               break;
+       default:
+               break;
+       }
+       max_mem = multiplier * atol(max_mem_string);
+       // max_mem should be checked that it was not zero after atol!
+       return max_mem;
+}
+
 int bam_sort(int argc, char *argv[])
 {
        size_t max_mem = 500000000;
@@ -426,7 +451,7 @@ int bam_sort(int argc, char *argv[])
                switch (c) {
                case 'o': is_stdout = 1; break;
                case 'n': is_by_qname = 1; break;
-               case 'm': max_mem = atol(optarg); break;
+               case 'm': max_mem = bam_sort_get_max_mem(optarg); break;
                }
        }
        if (optind + 2 > argc) {