Changeset: 15361647fecc for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=15361647fecc
Modified Files:
sql/backends/monet5/bam/bam_lib.c
Branch: bamloader
Log Message:
Improve seq_length_bat by direct appending instead of usign BUNappend and make
code of reverse_seq_bat and reverse_qual_bat more generic
diffs (296 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
@@ -283,15 +283,6 @@ seq_char(str * ret, int * ref_pos, str *
output->T->nonil = output->T->nonil && *cur_out != TPE##_nil; \
}
-#define update_props_str() { \
- output->tsorted = output->tsorted && \
- (c == 0 || strcmp(*cur_out, prev_out) >= 0); \
- output->trevsorted = output->trevsorted && \
- (c == 0 || strcmp(*cur_out, prev_out) <= 0); \
- output->T->nil = output->T->nil || *cur_out == str_nil; \
- output->T->nonil = output->T->nonil && *cur_out != str_nil; \
-}
-
#define finish_props() { \
BATsetcount(output, BATcount(input)); \
BATseqbase(output, input->hseqbase); \
@@ -344,221 +335,102 @@ bam_flag_bat(bat * ret, bat * bid, str *
return MAL_SUCCEED;
}
-/* Commented out, since string heap addition needs to be added
-str
-reverse_seq_bat(bat * ret, bat * bid)
-{
- BAT *input, *output;
- str prev_out = 0;
- str *cur_in;
- str *cur_out;
- BUN c;
- str msg;
-
- assert(ret != NULL && bid != NULL);
-
- if ((input = BATdescriptor(*bid)) == NULL)
- throw(MAL, "reverse_seq_bat", RUNTIME_OBJECT_MISSING);
-*/
- /* allocate result BAT */
-/* output = BATnew(TYPE_void, TYPE_str, BATcount(input), TRANSIENT);
- if (output == NULL) {
- throw(MAL, "reverse_seq_bat", MAL_MALLOC_FAIL);
- }
-
- init_props();
- cur_in = (str *) Tloc(input, BUNfirst(input));
- cur_out = (str *) Tloc(output, BUNfirst(output));
- for(c = 0; c < BATcount(input); ++c) {
- if ((msg = reverse_seq(cur_out, cur_in)) != MAL_SUCCEED) {
- BBPreleaseref(output->batCacheid);
- return msg;
- }
- update_props_str();
- cur_in++;
- prev_out = *cur_out++;
- }
- finish_props();
-*/
- /* release input BAT-descriptor */
-/* BBPreleaseref(input->batCacheid);
-
- BBPkeepref((*ret = output->batCacheid));
-
- return MAL_SUCCEED;
-}*/
+#define transform_strbat(transform_fn) { \
+ BAT *input, *output; \
+ BATiter li; \
+ BUN p = 0, q = 0; \
+ \
+ assert(ret != NULL && bid != NULL); \
+ \
+ if ((input = BATdescriptor(*bid)) == NULL) \
+ throw(MAL, "reverse_seq_bat", RUNTIME_OBJECT_MISSING); \
+ \
+ /* allocate result BAT */ \
+ output = BATnew(TYPE_void, TYPE_str, BATcount(input), TRANSIENT); \
+ if (output == NULL) { \
+ BBPreleaseref(input->batCacheid); \
+ throw(MAL, "reverse_seq_bat", MAL_MALLOC_FAIL); \
+ } \
+ BATseqbase(output, input->hseqbase); \
+ \
+ li = bat_iterator(input); \
+ \
+ BATloop(input, p, q) { \
+ str t = (str) BUNtail(li, p); \
+ str r, msg; \
+ \
+ if ((msg = transform_fn(&r, &t)) != MAL_SUCCEED) { \
+ BBPreleaseref(input->batCacheid); \
+ BBPreleaseref(output->batCacheid); \
+ return msg; \
+ } \
+ BUNappend(output, (ptr) r, FALSE); \
+ GDKfree(r); \
+ } \
+ \
+ /* release input BAT-descriptor */ \
+ BBPreleaseref(input->batCacheid); \
+ \
+ BBPkeepref((*ret = output->batCacheid)); \
+ \
+ return MAL_SUCCEED; \
+}
str
reverse_seq_bat(bat * ret, bat * bid)
{
- BAT *seqs, *result;
- BATiter li;
- BUN p = 0, q = 0;
-
- assert(ret != NULL && bid != NULL);
-
- if ((seqs = BATdescriptor(*bid)) == NULL)
- throw(MAL, "reverse_seq_bat", RUNTIME_OBJECT_MISSING);
-
- /* allocate result BAT */
- result = BATnew(TYPE_void, TYPE_str, BATcount(seqs), TRANSIENT);
- if (result == NULL) {
- BBPreleaseref(seqs->batCacheid);
- throw(MAL, "reverse_seq_bat", MAL_MALLOC_FAIL);
- }
- BATseqbase(result, seqs->hseqbase);
-
- li = bat_iterator(seqs);
-
- BATloop(seqs, p, q) {
- str t = (str) BUNtail(li, p);
- str r, msg;
-
- if ((msg = reverse_seq(&r, &t)) != MAL_SUCCEED) {
- BBPreleaseref(seqs->batCacheid);
- BBPreleaseref(result->batCacheid);
- return msg;
- }
- BUNappend(result, (ptr) r, FALSE);
- GDKfree(r);
- }
-
- /* release input BAT-descriptor */
- BBPreleaseref(seqs->batCacheid);
-
- BBPkeepref((*ret = result->batCacheid));
-
- return MAL_SUCCEED;
+ transform_strbat(reverse_seq);
}
str
reverse_qual_bat(bat * ret, bat * bid)
{
- BAT *quals, *result;
- BATiter li;
- BUN p = 0, q = 0;
-
- assert(ret != NULL && bid != NULL);
-
- if ((quals = BATdescriptor(*bid)) == NULL)
- throw(MAL, "reverse_qual_bat", RUNTIME_OBJECT_MISSING);
-
- /* allocate result BAT */
- result = BATnew(TYPE_void, TYPE_str, BATcount(quals), TRANSIENT);
- if (result == NULL) {
- BBPreleaseref(quals->batCacheid);
- throw(MAL, "reverse_qual_bat", MAL_MALLOC_FAIL);
- }
- BATseqbase(result, quals->hseqbase);
-
- li = bat_iterator(quals);
-
- BATloop(quals, p, q) {
- str t = (str) BUNtail(li, p);
- str r, msg;
-
- if ((msg = reverse_qual(&r, &t)) != MAL_SUCCEED) {
- BBPreleaseref(quals->batCacheid);
- BBPreleaseref(result->batCacheid);
- return msg;
- }
- BUNappend(result, (ptr) r, FALSE);
- GDKfree(r);
- }
-
- /* release input BAT-descriptor */
- BBPreleaseref(quals->batCacheid);
-
- BBPkeepref((*ret = result->batCacheid));
-
- return MAL_SUCCEED;
+ transform_strbat(reverse_qual);
}
-/*str Does not work, probably has to do with we not being able to traverse the
- CIGAR string input BAT like this
+str
seq_length_bat(bat * ret, bat * bid)
{
BAT *input, *output;
sht prev_out = 0;
- str *cur_in;
+ str cur_in;
int *cur_out;
- BUN c;
+ BATiter li;
+ BUN c = 0, p = 0, q = 0;
str msg;
assert(ret != NULL && bid != NULL);
if ((input = BATdescriptor(*bid)) == NULL)
throw(MAL, "seq_length_bat", RUNTIME_OBJECT_MISSING);
-*/
+
/* allocate result BAT */
-/* output = BATnew(TYPE_void, TYPE_int, BATcount(input), TRANSIENT);
+ output = BATnew(TYPE_void, TYPE_int, BATcount(input), TRANSIENT);
if (output == NULL) {
throw(MAL, "seq_length_bat", MAL_MALLOC_FAIL);
}
init_props();
- cur_in = (str *) Tloc(input, BUNfirst(input));
+ li = bat_iterator(input);
cur_out = (int *) Tloc(output, BUNfirst(output));
- for(c = 0; c < BATcount(input); ++c) {
- if ((msg = seq_length(cur_out, cur_in)) != MAL_SUCCEED) {
+ BATloop(input, p, q) {
+ cur_in = (str) BUNtail(li, p);
+ if ((msg = seq_length(cur_out, &cur_in)) != MAL_SUCCEED) {
BBPreleaseref(output->batCacheid);
return msg;
}
update_props(int);
- cur_in++;
+ ++c;
prev_out = *cur_out++;
}
finish_props();
-*/
+
/* release input BAT-descriptor */
-/* BBPreleaseref(input->batCacheid);
+ BBPreleaseref(input->batCacheid);
BBPkeepref((*ret = output->batCacheid));
return MAL_SUCCEED;
-}*/
-
-str
-seq_length_bat(bat * ret, bat * bid)
-{
- BAT *cigars, *result;
- BATiter li;
- BUN p = 0, q = 0;
-
- assert(ret != NULL && bid != NULL);
-
- if ((cigars = BATdescriptor(*bid)) == NULL)
- throw(MAL, "seq_length_bat", RUNTIME_OBJECT_MISSING);
-
- /* allocate result BAT */
- result = BATnew(TYPE_void, TYPE_int, BATcount(cigars), TRANSIENT);
- if (result == NULL) {
- BBPreleaseref(cigars->batCacheid);
- throw(MAL, "seq_length_bat", MAL_MALLOC_FAIL);
- }
- BATseqbase(result, cigars->hseqbase);
-
- li = bat_iterator(cigars);
-
- BATloop(cigars, p, q) {
- str t = (str) BUNtail(li, p);
- str msg;
- int r;
-
- if ((msg = seq_length(&r, &t)) != MAL_SUCCEED) {
- BBPreleaseref(cigars->batCacheid);
- BBPreleaseref(result->batCacheid);
- return msg;
- }
- BUNappend(result, (ptr) &r, FALSE);
- }
-
- /* release input BAT-descriptor */
- BBPreleaseref(cigars->batCacheid);
-
- BBPkeepref((*ret = result->batCacheid));
-
- return MAL_SUCCEED;
}
str
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