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Clarify bwa mem -5 option 

Clarify that the -5 bwa mem option chooses the alignment that starts earliest in the read relative to the read/sequencing order, not genomic coordinate order
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Nils Homer 2020-08-18 23:01:43 -07:00 committed by GitHub
parent 94ff6b297a
commit b58da139c3
1 changed files with 1 additions and 1 deletions
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fastmap.c
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@ -296,7 +296,7 @@ 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, " -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, " -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, " -K INT process INT input bases in each batch regardless of nThreads (for reproducibility) []\n");
fprintf(stderr, "\n");