Changeset: afdccf6751c0 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=afdccf6751c0
Modified Files:
sql/backends/monet5/bam/bam_lib.c
Branch: bamloader
Log Message:
Improved bam_flag bulk version by directly writing to BAT. Also attempted this
for other functions, but there are still problems with those so the old
versions are kept in tact.
diffs (195 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
@@ -229,16 +229,44 @@ seq_char(str * ret, int * ref_pos, str *
return MAL_SUCCEED;
}
+#define init_props() { \
+ output->tsorted = TRUE; \
+ output->trevsorted = TRUE; \
+}
+#define update_props(TPE) { \
+ output->tsorted = output->tsorted && \
+ (c == 0 || *cur_out >= prev_out); \
+ output->trevsorted = output->trevsorted && \
+ (c == 0 || *cur_out <= prev_out); \
+ output->T->nil = output->T->nil || *cur_out == TPE##_nil; \
+ 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); \
+ output->tkey = FALSE; /* Tail values are not unique */ \
+}
str
bam_flag_bat(bat * ret, bat * bid, str * name)
{
- BAT *flags, *result;
- BATiter li;
- BUN p = 0, q = 0;
+ BAT *input, *output;
+ sht prev_out = 0;
+ sht *cur_in;
+ bit *cur_out;
sht k;
+ BUN c;
assert(ret != NULL && bid != NULL && name != NULL);
@@ -247,33 +275,78 @@ bam_flag_bat(bat * ret, bat * bid, str *
throw(MAL, "bam_flag", "Unknown flag name given: %s\n",
*name);
- if ((flags = BATdescriptor(*bid)) == NULL)
+ if ((input = BATdescriptor(*bid)) == NULL)
throw(MAL, "bam_flag_bat", RUNTIME_OBJECT_MISSING);
/* allocate result BAT */
- result = BATnew(TYPE_void, TYPE_bit, BATcount(flags), TRANSIENT);
- if (result == NULL) {
+ output = BATnew(TYPE_void, TYPE_bit, BATcount(input), TRANSIENT);
+ if (output == NULL) {
throw(MAL, "bam_flag_bat", MAL_MALLOC_FAIL);
}
- BATseqbase(result, flags->hseqbase);
-
- li = bat_iterator(flags);
-
- BATloop(flags, p, q) {
- sht t = *(sht *) BUNtail(li, p);
- bit r = kth_bit(t, k);
-
- BUNappend(result, (ptr) &r, FALSE);
+
+ init_props();
+ cur_in = (sht *) Tloc(input, BUNfirst(input));
+ cur_out = (bit *) Tloc(output, BUNfirst(output));
+ for(c = 0; c < BATcount(input); ++c) {
+ *cur_out = kth_bit(*cur_in, k);
+ update_props(bit);
+ cur_in++;
+ prev_out = *cur_out++;
}
+ finish_props();
/* release input BAT-descriptor */
- BBPreleaseref(flags->batCacheid);
+ BBPreleaseref(input->batCacheid);
- BBPkeepref((*ret = result->batCacheid));
+ BBPkeepref((*ret = output->batCacheid));
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;
+}*/
+
str
reverse_seq_bat(bat * ret, bat * bid)
{
@@ -356,6 +429,50 @@ reverse_qual_bat(bat * ret, bat * bid)
return MAL_SUCCEED;
}
+/*str Does not work, probably has to do with we not being able to traverse the
+ CIGAR string input BAT like this
+seq_length_bat(bat * ret, bat * bid)
+{
+ BAT *input, *output;
+ sht prev_out = 0;
+ str *cur_in;
+ int *cur_out;
+ BUN c;
+ 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);
+ if (output == NULL) {
+ throw(MAL, "seq_length_bat", MAL_MALLOC_FAIL);
+ }
+
+ init_props();
+ cur_in = (str *) Tloc(input, BUNfirst(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) {
+ BBPreleaseref(output->batCacheid);
+ return msg;
+ }
+ update_props(int);
+ cur_in++;
+ prev_out = *cur_out++;
+ }
+ finish_props();
+*/
+ /* release input BAT-descriptor */
+/* BBPreleaseref(input->batCacheid);
+
+ BBPkeepref((*ret = output->batCacheid));
+
+ return MAL_SUCCEED;
+}*/
+
str
seq_length_bat(bat * ret, bat * bid)
{
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