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SAM TLEN should be 0 when either read is unmapped 

this_rid/this_pos will be copied from r_prev(=r_next)'s values when this
read is unmapped (i.e., r is NULL). In this case, we can write RNEXT as
'=' but should not calculate TLEN from these placeholder values.
Similarly when the mate is unmapped (i.e., r_next is NULL).

Fixes #365.
This commit is contained in:
John Marshall 2019-04-04 11:14:07 +01:00 committed by Heng Li
parent 169216bfff
commit 371bc9513a
1 changed files with 5 additions and 5 deletions
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10
format.c
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@ -460,17 +460,17 @@ void mm_write_sam3(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
int tlen = 0;
if (this_rid >= 0 && r_next) {
if (this_rid == r_next->rid) {
int this_pos5 = r && r->rev? r->re - 1 : this_pos;
int next_pos5 = r_next->rev? r_next->re - 1 : r_next->rs;
tlen = next_pos5 - this_pos5;
if (r) {
int this_pos5 = r->rev? r->re - 1 : this_pos;
int next_pos5 = r_next->rev? r_next->re - 1 : r_next->rs;
tlen = next_pos5 - this_pos5;
}
mm_sprintf_lite(s, "\t=\t");
} else mm_sprintf_lite(s, "\t%s\t", mi->seq[r_next->rid].name);
mm_sprintf_lite(s, "%d\t", r_next->rs + 1);
} else if (r_next) { // && this_rid < 0
mm_sprintf_lite(s, "\t%s\t%d\t", mi->seq[r_next->rid].name, r_next->rs + 1);
} else if (this_rid >= 0) { // && r_next == NULL
int this_pos5 = this_rev? r->re - 1 : this_pos; // this_rev is only true when r != NULL
tlen = this_pos - this_pos5; // next_pos5 will be this_pos
mm_sprintf_lite(s, "\t=\t%d\t", this_pos + 1); // next segment will take r's coordinate
} else mm_sprintf_lite(s, "\t*\t0\t"); // neither has coordinates
if (tlen > 0) ++tlen;