#include "bam2bcf.h"
#include "ksort.h"
#include "kaln.h"
+#include "kprobaln.h"
#include "khash.h"
KHASH_SET_INIT_STR(rg)
for (l = qbeg; l < qend; ++l)
query[l - qbeg] = bam_nt16_nt4_table[bam1_seqi(seq, l)];
// do alignment; this takes most of computing time for indel calling
- sc = ka_global_score((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
- (uint8_t*)query, qend - qbeg, &ap);
- score[K*n_types + t] = -sc;
+ if (0) {
+ uint8_t *qq = calloc(qend - qbeg, 1);
+ for (l = 0; l < qend - qbeg; ++l) qq[l] = 23;
+ sc = kpa_glocal((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
+ (uint8_t*)query, qend - qbeg, qq, &kpa_par_alt, 0, 0);
+ score[K*n_types + t] = sc;
+ } else {
+ sc = ka_global_score((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
+ (uint8_t*)query, qend - qbeg, &ap);
+ score[K*n_types + t] = -sc;
+ }
/*
for (l = 0; l < tend - tbeg + abs(types[t]); ++l)
fputc("ACGTN"[(int)ref2[tbeg-left+l]], stderr);