Changeset: fc49bc387cc1 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=fc49bc387cc1
Modified Files:
sql/backends/monet5/bamloader/bam_lib.c
Branch: bamloader
Log Message:
Fixed BAM library
diffs (122 lines):
diff --git a/sql/backends/monet5/bamloader/bam_lib.c
b/sql/backends/monet5/bamloader/bam_lib.c
--- a/sql/backends/monet5/bamloader/bam_lib.c
+++ b/sql/backends/monet5/bamloader/bam_lib.c
@@ -112,6 +112,7 @@ reverse_seq(str * ret, str * seq)
result[len - i - 1] = 'N';
break;
default:
+ GDKfree(result);
throw(MAL, "reverse_seq",
"Invalid character found in sequence: '%c'\n",
(*seq)[i]);
@@ -189,7 +190,7 @@ bam_flag_bat(bat * ret, bat * bid, str *
throw(MAL, "bam_flag_bat", RUNTIME_OBJECT_MISSING);
/* allocate result BAT */
- result = BATnew(TYPE_oid, TYPE_bit, BATcount(flags));
+ result = BATnew(TYPE_void, TYPE_bit, BATcount(flags));
if (result == NULL) {
throw(MAL, "bam_flag_bat", MAL_MALLOC_FAIL);
}
@@ -198,13 +199,10 @@ bam_flag_bat(bat * ret, bat * bid, str *
li = bat_iterator(flags);
BATloop(flags, p, q) {
- ptr h = BUNhead(li, p);
sht t = *(sht *) BUNtail(li, p);
bit r = kth_bit(t, k);
- /* insert original head and the right flag in result BAT */
- /* BUNins() takes care of all necessary administration */
- BUNins(result, h, (ptr) & r, FALSE);
+ BUNappend(result, (ptr) &r, FALSE);
}
/* release input BAT-descriptor */
@@ -228,7 +226,7 @@ reverse_seq_bat(bat * ret, bat * bid)
throw(MAL, "reverse_seq_bat", RUNTIME_OBJECT_MISSING);
/* allocate result BAT */
- result = BATnew(TYPE_oid, TYPE_str, BATcount(seqs));
+ result = BATnew(TYPE_void, TYPE_str, BATcount(seqs));
if (result == NULL) {
throw(MAL, "reverse_seq_bat", MAL_MALLOC_FAIL);
}
@@ -237,7 +235,6 @@ reverse_seq_bat(bat * ret, bat * bid)
li = bat_iterator(seqs);
BATloop(seqs, p, q) {
- ptr h = BUNhead(li, p);
str t = (str) BUNtail(li, p);
str r, msg;
@@ -245,10 +242,7 @@ reverse_seq_bat(bat * ret, bat * bid)
BBPreleaseref(result->batCacheid);
return msg;
}
- /* insert original head and the reversed sequence in
- * result BAT */
- /* BUNins() takes care of all necessary administration */
- BUNins(result, h, (ptr) r, FALSE);
+ BUNappend(result, (ptr) r, FALSE);
GDKfree(r);
}
@@ -273,7 +267,7 @@ reverse_qual_bat(bat * ret, bat * bid)
throw(MAL, "reverse_qual_bat", RUNTIME_OBJECT_MISSING);
/* allocate result BAT */
- result = BATnew(TYPE_oid, TYPE_str, BATcount(quals));
+ result = BATnew(TYPE_void, TYPE_str, BATcount(quals));
if (result == NULL) {
throw(MAL, "reverse_qual_bat", MAL_MALLOC_FAIL);
}
@@ -282,7 +276,6 @@ reverse_qual_bat(bat * ret, bat * bid)
li = bat_iterator(quals);
BATloop(quals, p, q) {
- ptr h = BUNhead(li, p);
str t = (str) BUNtail(li, p);
str r, msg;
@@ -290,10 +283,7 @@ reverse_qual_bat(bat * ret, bat * bid)
BBPreleaseref(result->batCacheid);
return msg;
}
- /* insert original head and the reversed sequence in
- * result BAT */
- /* BUNins() takes care of all necessary administration */
- BUNins(result, h, (ptr) r, FALSE);
+ BUNappend(result, (ptr) r, FALSE);
GDKfree(r);
}
@@ -318,7 +308,7 @@ seq_length_bat(bat * ret, bat * bid)
throw(MAL, "seq_length_bat", RUNTIME_OBJECT_MISSING);
/* allocate result BAT */
- result = BATnew(TYPE_oid, TYPE_int, BATcount(cigars));
+ result = BATnew(TYPE_void, TYPE_int, BATcount(cigars));
if (result == NULL) {
throw(MAL, "seq_length_bat", MAL_MALLOC_FAIL);
}
@@ -327,7 +317,6 @@ seq_length_bat(bat * ret, bat * bid)
li = bat_iterator(cigars);
BATloop(cigars, p, q) {
- ptr h = BUNhead(li, p);
str t = (str) BUNtail(li, p);
str msg;
int r;
@@ -336,10 +325,7 @@ seq_length_bat(bat * ret, bat * bid)
BBPreleaseref(result->batCacheid);
return msg;
}
- /* insert original head and the reversed sequence in
- * result BAT */
- /* BUNins() takes care of all necessary administration */
- BUNins(result, h, (ptr) & r, FALSE);
+ BUNappend(result, (ptr) &r, FALSE);
}
/* release input BAT-descriptor */
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