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r985: optionally report cs/cg on the query strand

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PAF only; not well tested
This commit is contained in:
Heng Li
2020-04-21 12:37:35 -04:00
parent 29f67a1666
commit da7109fd29
9 changed files with 114 additions and 42 deletions
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options.c
+5
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@@ -191,5 +191,10 @@ int mm_check_opt(const mm_idxopt_t *io, const mm_mapopt_t *mo)
fprintf(stderr, "[ERROR]\033[1;31m -X/-P and --secondary=no can't be applied at the same time\033[0m\n");
return -5;
}
if ((mo->flag & MM_F_QSTRAND) && ((mo->flag & (MM_F_OUT_SAM|MM_F_SPLICE|MM_F_FRAG_MODE)) || (io->flag & MM_I_HPC))) {
if (mm_verbose >= 1)
fprintf(stderr, "[ERROR]\033[1;31m --qstrand doesn't work with -a, -H, --frag or --splice\033[0m\n");
return -5;
}
return 0;
}