Changeset: 652329ec295a for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=652329ec295a
Modified Files:
sql/backends/monet5/bam/bam.mal
sql/backends/monet5/bam/bam_lib.c
Branch: bamloader
Log Message:
Revert bam_lib.c and bam.mal back to their previous bulk operator for seq_char
diffs (167 lines):
diff --git a/sql/backends/monet5/bam/bam.mal b/sql/backends/monet5/bam/bam.mal
--- a/sql/backends/monet5/bam/bam.mal
+++ b/sql/backends/monet5/bam/bam.mal
@@ -53,7 +53,9 @@ pattern bam_export(output_path:str):void
address bam_exportf
comment "Export results in the bam.export table to a BAM file"
+
# BAT signatures for bam_lib
+
module batbam;
command bam_flag(flags:bat[:oid,:sht], name:str):bat[:oid,:bit]
@@ -72,6 +74,6 @@ command seq_length(cigars:bat[:oid,:str]
address seq_length_bat
comment "Calculate the real length of a bat of DNA sequences, given their
CIGAR string."
-command seq_char(ref_pos:bat[:oid,:int], alg_seq:bat[:oid,:str],
alg_pos:bat[:oid,:int], alg_cigar:bat[:oid,:str]):bat[:oid,:str]
+command seq_char(ref_pos:int, alg_seq:bat[:oid,:str], alg_pos:bat[:oid,:int],
alg_cigar:bat[:oid,:str]):bat[:oid,:str]
address seq_char_bat
comment "Calculate the character in the alignment string (alg_str) that is
aligned to position 'ref_pos', conforming to the given cigar string (bat based
version)"
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
@@ -54,7 +54,6 @@ bam_flag(bit * ret, sht * flag, str * na
return MAL_SUCCEED;
}
-// use a simple lookup table for these mappings
str
reverse_seq(str * ret, str * seq)
{
@@ -254,7 +253,6 @@ bam_flag_bat(bat * ret, bat * bid, str *
/* allocate result BAT */
result = BATnew(TYPE_void, TYPE_bit, BATcount(flags), TRANSIENT);
if (result == NULL) {
- BBPreleaseref(flags->batCacheid);
throw(MAL, "bam_flag_bat", MAL_MALLOC_FAIL);
}
BATseqbase(result, flags->hseqbase);
@@ -291,7 +289,6 @@ reverse_seq_bat(bat * ret, bat * bid)
/* 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);
@@ -304,7 +301,6 @@ reverse_seq_bat(bat * ret, bat * bid)
if ((msg = reverse_seq(&r, &t)) != MAL_SUCCEED) {
BBPreleaseref(result->batCacheid);
- BBPreleaseref(seqs->batCacheid);
return msg;
}
BUNappend(result, (ptr) r, FALSE);
@@ -334,7 +330,6 @@ reverse_qual_bat(bat * ret, bat * bid)
/* 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);
@@ -346,7 +341,6 @@ reverse_qual_bat(bat * ret, bat * bid)
str r, msg;
if ((msg = reverse_qual(&r, &t)) != MAL_SUCCEED) {
- BBPreleaseref(quals->batCacheid);
BBPreleaseref(result->batCacheid);
return msg;
}
@@ -377,7 +371,6 @@ seq_length_bat(bat * ret, bat * bid)
/* 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);
@@ -391,7 +384,6 @@ seq_length_bat(bat * ret, bat * bid)
if ((msg = seq_length(&r, &t)) != MAL_SUCCEED) {
BBPreleaseref(result->batCacheid);
- BBPreleaseref(cigars->batCacheid);
return msg;
}
BUNappend(result, (ptr) &r, FALSE);
@@ -409,26 +401,18 @@ seq_length_bat(bat * ret, bat * bid)
str
seq_char_bat(bat * ret, int * ref_pos, bat * alg_seq, bat * alg_pos, bat *
alg_cigar)
{
- BAT *seqs = NULL, *poss = NULL, *refs = NULL, *cigars = NULL, *result =
NULL;
- BUN ref= 0, seq = 0, pos = 0, cigar = 0, seq_end = 0;
- BATiter ref_it, seq_it, pos_it, cigar_it;
+ BAT *seqs, *poss, *cigars, *result;
+ BUN seq = 0, pos = 0, cigar = 0, seq_end = 0;
+ BATiter seq_it, pos_it, cigar_it;
assert(ret != NULL && ref_pos != NULL && alg_seq != NULL && alg_pos !=
NULL && alg_cigar != NULL);
if ((seqs = BATdescriptor(*alg_seq)) == NULL ||
(poss = BATdescriptor(*alg_pos)) == NULL ||
- (refs = BATdescriptor(*ref_pos)) == NULL ||
- (cigars = BATdescriptor(*alg_cigar)) == NULL) {
- if( seqs) BBPreleaseref(seqs->batCacheid);
- if( poss) BBPreleaseref(poss->batCacheid);
- if( refs) BBPreleaseref(refs->batCacheid);
- throw(MAL, "seq_char_bat", RUNTIME_OBJECT_MISSING);
- }
+ (cigars = BATdescriptor(*alg_cigar)) == NULL)
+ throw(MAL, "seq_char_bat", RUNTIME_OBJECT_MISSING);
if(BATcount(seqs) != BATcount(poss) || BATcount(seqs) !=
BATcount(cigars)) {
- BBPreleaseref(seqs->batCacheid);
- BBPreleaseref(poss->batCacheid);
- BBPreleaseref(refs->batCacheid);
throw(MAL, "seq_char_bat",
"Misalignment in input BATs: "BUNFMT"/"BUNFMT"/"BUNFMT,
BATcount(poss), BATcount(seqs), BATcount(cigars));
@@ -437,37 +421,27 @@ seq_char_bat(bat * ret, int * ref_pos, b
/* allocate result BAT */
result = BATnew(TYPE_void, TYPE_str, BATcount(cigars), TRANSIENT);
if (result == NULL) {
- BBPreleaseref(seqs->batCacheid);
- BBPreleaseref(poss->batCacheid);
- BBPreleaseref(refs->batCacheid);
throw(MAL, "seq_char_bat", MAL_MALLOC_FAIL);
}
BATseqbase(result, seqs->hseqbase);
- ref = BUNfirst(refs);
seq = BUNfirst(seqs);
pos = BUNfirst(poss);
cigar = BUNfirst(cigars);
seq_end = BUNlast(seqs);
- ref_it = bat_iterator(refs);
seq_it = bat_iterator(seqs);
pos_it = bat_iterator(poss);
cigar_it = bat_iterator(cigars);
while(seq < seq_end) {
str seq_val = (str) BUNtail(seq_it, seq);
- int * ref_val = (int *) BUNtail(ref_it, ref);
int * pos_val = (int *) BUNtail(pos_it, pos);
str cigar_val = (str) BUNtail(cigar_it, cigar);
str r;
str msg;
- if ((msg = seq_char(&r, ref_val, &seq_val, pos_val,
&cigar_val)) != MAL_SUCCEED) {
- BBPreleaseref(refs->batCacheid);
- BBPreleaseref(seqs->batCacheid);
- BBPreleaseref(poss->batCacheid);
- BBPreleaseref(cigars->batCacheid);
+ if ((msg = seq_char(&r, ref_pos, &seq_val, pos_val,
&cigar_val)) != MAL_SUCCEED) {
BBPreleaseref(result->batCacheid);
return msg;
}
@@ -478,7 +452,6 @@ seq_char_bat(bat * ret, int * ref_pos, b
}
/* release input BAT-descriptors */
- BBPreleaseref(refs->batCacheid);
BBPreleaseref(seqs->batCacheid);
BBPreleaseref(poss->batCacheid);
BBPreleaseref(cigars->batCacheid);
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