Changeset: 66ed214f01d6 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=66ed214f01d6
Modified Files:
sql/backends/monet5/bam/bam.mal
sql/backends/monet5/bam/bam_lib.c
Branch: bamloader
Log Message:
An alternative bulk version for the seq_char
Also made mode robust against errors
diffs (103 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
@@ -53,9 +53,7 @@ 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]
@@ -74,6 +72,6 @@ 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:int, alg_seq:bat[:oid,:str], alg_pos:bat[:oid,:int],
alg_cigar:bat[:oid,:str]):bat[:oid,:str]
+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]
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
@@ -401,18 +401,26 @@ 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, *poss, *cigars, *result;
- BUN seq = 0, pos = 0, cigar = 0, seq_end = 0;
- BATiter seq_it, pos_it, cigar_it;
+ BAT *seqs, *poss, *refs, *cigars, *result;
+ BUN ref= 0, seq = 0, pos = 0, cigar = 0, seq_end = 0;
+ BATiter ref_it, 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 ||
- (cigars = BATdescriptor(*alg_cigar)) == NULL)
- throw(MAL, "seq_char_bat", RUNTIME_OBJECT_MISSING);
+ (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);
+ }
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));
@@ -421,27 +429,37 @@ 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_pos, &seq_val, pos_val,
&cigar_val)) != MAL_SUCCEED) {
+ 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);
BBPreleaseref(result->batCacheid);
return msg;
}
@@ -452,6 +470,7 @@ 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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