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r967: no duplicated @SQ lines with --split-prefix

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resolves #527 and #400
This commit is contained in:
Heng Li
2020-01-18 12:01:28 -05:00
parent 04e015d803
commit 24f50f38e8
1 changed files with 5 additions and 2 deletions
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main.c
+5 -2
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@@ -7,7 +7,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "ketopt.h" #include "ketopt.h"
#define MM_VERSION "2.17-r966-dirty" #define MM_VERSION "2.17-r967-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>
@@ -361,7 +361,10 @@ int main(int argc, char *argv[])
} }
if ((opt.flag & MM_F_OUT_SAM) && idx_rdr->n_parts == 1) { if ((opt.flag & MM_F_OUT_SAM) && idx_rdr->n_parts == 1) {
if (mm_idx_reader_eof(idx_rdr)) { if (mm_idx_reader_eof(idx_rdr)) {
ret = mm_write_sam_hdr(mi, rg, MM_VERSION, argc, argv); if (opt.split_prefix == 0)
ret = mm_write_sam_hdr(mi, rg, MM_VERSION, argc, argv);
else
ret = mm_write_sam_hdr(0, rg, MM_VERSION, argc, argv);
} else { } else {
ret = mm_write_sam_hdr(0, rg, MM_VERSION, argc, argv); ret = mm_write_sam_hdr(0, rg, MM_VERSION, argc, argv);
if (opt.split_prefix == 0 && mm_verbose >= 2) if (opt.split_prefix == 0 && mm_verbose >= 2)