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r962: abort given wrong RG line; resolves #541

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This commit is contained in:
Heng Li
2020-01-06 21:53:21 -05:00
parent 47b646acbf
commit 3c0d05d272
3 changed files with 18 additions and 8 deletions
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main.c
+9 -3
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@@ -7,7 +7,7 @@
#include "mmpriv.h"
#include "ketopt.h"
#define MM_VERSION "2.17-r961-dirty"
#define MM_VERSION "2.17-r962-dirty"
#ifdef __linux__
#include <sys/resource.h>
@@ -356,13 +356,19 @@ int main(int argc, char *argv[])
return 1;
}
if ((opt.flag & MM_F_OUT_SAM) && idx_rdr->n_parts == 1) {
int ret;
if (mm_idx_reader_eof(idx_rdr)) {
mm_write_sam_hdr(mi, rg, MM_VERSION, argc, argv);
ret = mm_write_sam_hdr(mi, rg, MM_VERSION, argc, argv);
} else {
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)
fprintf(stderr, "[WARNING]\033[1;31m For a multi-part index, no @SQ lines will be outputted. Please use --split-prefix.\033[0m\n");
}
if (ret != 0) {
mm_idx_destroy(mi);
mm_idx_reader_close(idx_rdr);
return 1;
}
}
if (mm_verbose >= 3)
fprintf(stderr, "[M::%s::%.3f*%.2f] loaded/built the index for %d target sequence(s)\n",