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multi-seg working on toy examples

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Heng Li
2017-09-25 13:42:04 -04:00
parent a742f10164
commit 3bb66e1ed3
6 changed files with 62 additions and 16 deletions
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format.c
+2 -12
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@@ -213,17 +213,6 @@ void mm_write_paf(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const m
write_cs(km, s, mi, t, r);
}
static char comp_tab[] = {
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63,
64, 'T', 'V', 'G', 'H', 'E', 'F', 'C', 'D', 'I', 'J', 'M', 'L', 'K', 'N', 'O',
'P', 'Q', 'Y', 'S', 'A', 'A', 'B', 'W', 'X', 'R', 'Z', 91, 92, 93, 94, 95,
64, 't', 'v', 'g', 'h', 'e', 'f', 'c', 'd', 'i', 'j', 'm', 'l', 'k', 'n', 'o',
'p', 'q', 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 'z', 123, 124, 125, 126, 127
};
void mm_write_sam_SQ(const mm_idx_t *idx)
{
uint32_t i;
@@ -233,12 +222,13 @@ void mm_write_sam_SQ(const mm_idx_t *idx)
static void sam_write_sq(kstring_t *s, char *seq, int l, int rev, int comp)
{
extern unsigned char seq_comp_table[256];
if (rev) {
int i;
str_enlarge(s, l);
for (i = 0; i < l; ++i) {
int c = seq[l - 1 - i];
s->s[s->l + i] = c < 128 && comp? comp_tab[c] : c;
s->s[s->l + i] = c < 128 && comp? seq_comp_table[c] : c;
}
s->l += l;
} else str_copy(s, seq, seq + l);