Changeset: 3ed973da6129 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=3ed973da6129
Modified Files:
sql/backends/monet5/bam/bam_lib.c
Branch: bamloader
Log Message:
Make seq_char also work properly on insertions/deletions that occur in the
CIGAR string. Furthermore, add some extra error checks
diffs (114 lines):
diff --git a/sql/backends/monet5/bam/bam_lib.c
b/sql/backends/monet5/bam/bam_lib.c
--- a/sql/backends/monet5/bam/bam_lib.c
+++ b/sql/backends/monet5/bam/bam_lib.c
@@ -146,7 +146,8 @@ seq_length(int * ret, str * cigar)
int result = 0;
str cigar_consumable = *cigar;
- if (cigar_consumable[0] == '*' && cigar_consumable[1] == '\0') {
+ if (cigar_consumable[0] == '\0' ||
+ (cigar_consumable[0] == '*' && cigar_consumable[1] ==
'\0')) {
*ret = -1;
return MAL_SUCCEED;
}
@@ -173,44 +174,58 @@ str
seq_char(str * ret, int * ref_pos, str * alg_seq, int * alg_pos, str *
alg_cigar)
{
str cigar_consumable = *alg_cigar;
- int seq_pos = 0;
- bit at_character = false;
- int iterate_until = *ref_pos - *alg_pos;
- str result;
-
- if((result = GDKmalloc(2 * sizeof(char))) == NULL) {
- throw(MAL, "seq_char", MAL_MALLOC_FAIL);
- }
- result[1] = '\0';
+ int seq_pos = -1;
+ int cur_ref_pos = *alg_pos - 1;
- if (cigar_consumable[0] == '*' && cigar_consumable[1] == '\0') {
- result[0] = '\0';
- *ret = result;
+ if (cigar_consumable[0] == '\0' ||
+ (cigar_consumable[0] == '*' && cigar_consumable[1] ==
'\0')) {
+ *ret = GDKstrdup(str_nil);
return MAL_SUCCEED;
}
- while(cigar_consumable[0] != '\0' && seq_pos < iterate_until) {
+ while(TRUE) {
int cnt;
char op;
int nr_chars_read;
+ bit advance_ref_pos;
+ bit advance_seq_pos;
if (sscanf
(cigar_consumable, "%d%c%n", &cnt, &op,
&nr_chars_read) != 2)
throw(MAL, "seq_char",
"Error parsing CIGAR string '%s'\n",
*alg_cigar);
- if (op == 'M' || op == 'D' || op == 'N' || op == '='
- || op == 'X') {
+ advance_ref_pos = (op == 'M' || op == 'D' ||
+ op == 'N' || op == '=' || op == 'X');
+ advance_seq_pos = (op == 'M' || op == 'I'); // TODO: Find out
which chars advance the seq pos
+ if(advance_seq_pos) {
seq_pos += cnt;
- if(seq_pos > iterate_until)
- seq_pos = iterate_until;
- at_character = true;
- } else {
- at_character = false;
+ }
+ if (advance_ref_pos) {
+ cur_ref_pos += cnt;
+ if(cur_ref_pos >= *ref_pos) {
+ if(!advance_seq_pos) {
+ seq_pos = -1;
+ } else {
+ seq_pos -= (cur_ref_pos - *ref_pos);
+ }
+ break;
+ }
}
cigar_consumable += nr_chars_read;
+ if(cigar_consumable[0] == '\0') {
+ seq_pos = -1;
+ break;
+ }
}
- result[0] = at_character ? (*alg_seq)[seq_pos] : '\0';
- *ret = result;
+ if(seq_pos < 0 || seq_pos >= (int)strlen(*alg_seq)) {
+ *ret = GDKstrdup(str_nil);
+ return MAL_SUCCEED;
+ }
+ if(((*ret) = GDKmalloc(2 * sizeof(char))) == NULL) {
+ throw(MAL, "seq_char", MAL_MALLOC_FAIL);
+ }
+ (*ret)[0] = (*alg_seq)[seq_pos];
+ (*ret)[1] = '\0';
return MAL_SUCCEED;
}
@@ -398,7 +413,9 @@ seq_char_bat(bat * ret, int * ref_pos, b
throw(MAL, "seq_char_bat", RUNTIME_OBJECT_MISSING);
if(BATcount(seqs) != BATcount(poss) || BATcount(seqs) !=
BATcount(cigars)) {
- throw(MAL, "seq_char_bat", "Misalignment in input BATs");
+ throw(MAL, "seq_char_bat",
+ "Misalignment in input BATs: "BUNFMT"/"BUNFMT"/"BUNFMT,
+ BATcount(poss), BATcount(seqs), BATcount(cigars));
}
/* allocate result BAT */
@@ -428,7 +445,7 @@ seq_char_bat(bat * ret, int * ref_pos, b
BBPreleaseref(result->batCacheid);
return msg;
}
- BUNappend(result, (ptr) &r, FALSE);
+ BUNappend(result, (ptr) r, FALSE);
++seq;
++pos;
++cigar;
_______________________________________________
checkin-list mailing list
checkin-list@monetdb.org
https://www.monetdb.org/mailman/listinfo/checkin-list
