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r1234: added splice:sr for SE RNA-seq

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Heng Li
2025-03-30 15:54:12 -04:00
parent 2857de7dbd
commit 54f8e5f7d6
4 changed files with 10 additions and 3 deletions
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options.c
+7 -1
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@@ -174,8 +174,14 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
mo->junc_bonus = 9;
mo->junc_pen = 5;
mo->zdrop = 200, mo->zdrop_inv = 100; // because mo->a is halved
if (strcmp(preset, "splice:hq") == 0)
if (strcmp(preset, "splice:hq") == 0) {
mo->noncan = 5, mo->b = 4, mo->q = 6, mo->q2 = 24;
} else if (strcmp(preset, "splice:sr") == 0) {
mo->flag |= MM_F_NO_PRINT_2ND | MM_F_2_IO_THREADS | MM_F_HEAP_SORT;
mo->noncan = 5, mo->b = 4, mo->q = 6, mo->q2 = 24;
mo->end_bonus = 10;
mo->mini_batch_size = 50000000;
}
} else return -1;
return 0;
}