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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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hit.c
+1 -1
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@@ -55,7 +55,7 @@ mm_reg1_t *mm_gen_regs(void *km, uint32_t hash, int qlen, int n_u, uint64_t *u,
mm_reg1_t *r; mm_reg1_t *r;
int i, k; int i, k;
if (n_u == 0) return 0; if (n_u <= 0) return 0;
// sort by score // sort by score
z = (mm128_t*)kmalloc(km, n_u * 16); z = (mm128_t*)kmalloc(km, n_u * 16);
main.c
+1
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@@ -373,6 +373,7 @@ int main(int argc, char *argv[])
fprintf(fp_help, " --MD output the MD tag\n"); fprintf(fp_help, " --MD output the MD tag\n");
fprintf(fp_help, " --eqx write =/X CIGAR operators\n"); fprintf(fp_help, " --eqx write =/X CIGAR operators\n");
fprintf(fp_help, " -Y use soft clipping for supplementary alignments\n"); fprintf(fp_help, " -Y use soft clipping for supplementary alignments\n");
fprintf(fp_help, " -y copy FASTA/Q comments to output SAM\n");
fprintf(fp_help, " -t INT number of threads [%d]\n", n_threads); fprintf(fp_help, " -t INT number of threads [%d]\n", n_threads);
fprintf(fp_help, " -K NUM minibatch size for mapping [500M]\n"); fprintf(fp_help, " -K NUM minibatch size for mapping [500M]\n");
// fprintf(fp_help, " -v INT verbose level [%d]\n", mm_verbose); // fprintf(fp_help, " -v INT verbose level [%d]\n", mm_verbose);
minimap.h
+1 -1
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@@ -5,7 +5,7 @@
#include <stdio.h> #include <stdio.h>
#include <sys/types.h> #include <sys/types.h>
#define MM_VERSION "2.28-r1221-dirty" #define MM_VERSION "2.28-r1234-dirty"
#define MM_F_NO_DIAG (0x001LL) // no exact diagonal hit #define MM_F_NO_DIAG (0x001LL) // no exact diagonal hit
#define MM_F_NO_DUAL (0x002LL) // skip pairs where query name is lexicographically larger than target name #define MM_F_NO_DUAL (0x002LL) // skip pairs where query name is lexicographically larger than target name
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_bonus = 9;
mo->junc_pen = 5; mo->junc_pen = 5;
mo->zdrop = 200, mo->zdrop_inv = 100; // because mo->a is halved 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; 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; } else return -1;
return 0; return 0;
} }