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r369: updated example with the latest API

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This commit is contained in:
Heng Li
2017-09-14 22:44:10 -04:00
parent 75ff7ceec5
commit 14b853499f
2 changed files with 36 additions and 38 deletions
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main.c
+3 -4
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@@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.1.1-r368-dirty"
#define MM_VERSION "2.1.1-r369-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -67,6 +67,7 @@ int main(int argc, char *argv[])
char *fnw = 0, *rg = 0, *s;
FILE *fp_help = stderr;
mm_idx_reader_t *idx_rdr;
mm_idx_t *mi;
liftrlimit();
mm_realtime0 = realtime();
@@ -210,9 +211,7 @@ int main(int argc, char *argv[])
}
if (opt.flag & MM_F_OUT_SAM)
mm_write_sam_hdr_no_SQ(rg, MM_VERSION, argc, argv);
for (;;) {
mm_idx_t *mi;
if ((mi = mm_idx_reader_read(idx_rdr, n_threads)) == 0) break;
while ((mi = mm_idx_reader_read(idx_rdr, n_threads)) != 0) {
if (mm_verbose >= 2 && idx_rdr->n_parts > 1 && (opt.flag&MM_F_OUT_SAM) && !(opt.flag&MM_F_NO_SAM_SQ))
fprintf(stderr, "[WARNING] \033[1;31mSAM output is malformated due to internal @SQ lines. Please add option --no-sam-sq or filter afterwards.\033[0m\n");
if (mm_verbose >= 3)