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Merge pull request #297 from nh13/patch-3 

Clarify bwa mem -5 option
This commit is contained in:
Heng Li 2022-03-06 18:12:09 -05:00 committed by GitHub
parent d26eb2d288 b58da139c3
commit 4d8fb2ca91
1 changed files with 1 additions and 1 deletions
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fastmap.c
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@ -297,7 +297,7 @@ int main_mem(int argc, char *argv[])
fprintf(stderr, " -H STR/FILE insert STR to header if it starts with @; or insert lines in FILE [null]\n"); fprintf(stderr, " -H STR/FILE insert STR to header if it starts with @; or insert lines in FILE [null]\n");
fprintf(stderr, " -o FILE sam file to output results to [stdout]\n"); fprintf(stderr, " -o FILE sam file to output results to [stdout]\n");
fprintf(stderr, " -j treat ALT contigs as part of the primary assembly (i.e. ignore <idxbase>.alt file)\n"); fprintf(stderr, " -j treat ALT contigs as part of the primary assembly (i.e. ignore <idxbase>.alt file)\n");
fprintf(stderr, " -5 for split alignment, take the alignment with the smallest coordinate as primary\n"); fprintf(stderr, " -5 for split alignment, take the alignment with the smallest query (not genomic) coordinate as primary\n");
fprintf(stderr, " -q don't modify mapQ of supplementary alignments\n"); fprintf(stderr, " -q don't modify mapQ of supplementary alignments\n");
fprintf(stderr, " -K INT process INT input bases in each batch regardless of nThreads (for reproducibility) []\n"); fprintf(stderr, " -K INT process INT input bases in each batch regardless of nThreads (for reproducibility) []\n");
fprintf(stderr, "\n"); fprintf(stderr, "\n");