Changeset: 95104df7abc8 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=95104df7abc8
Modified Files:
sql/backends/monet5/bam/bam_lib.c
Branch: bamloader
Log Message:
Treat "=" character in CIGAR string as the "m" character when calculating
seq_char
diffs (38 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
@@ -196,7 +196,7 @@ seq_char(str * ret, int * ref_pos, str *
"Error parsing CIGAR string '%s'\n",
*alg_cigar);
advance_ref_pos = (op == 'M' || op == 'D' ||
op == 'N' || op == '=' || op == 'X');
- advance_seq_pos = (op == 'M' || op == 'I'); // TODO: Find out
which chars advance the seq pos
+ advance_seq_pos = (op == 'M' || op == 'I' || op == '='); //
TODO: Find out which chars advance the seq pos
if(advance_seq_pos) {
seq_pos += cnt;
}
@@ -397,7 +397,6 @@ seq_length_bat(bat * ret, bat * bid)
return MAL_SUCCEED;
}
-
str
seq_char_bat(bat * ret, int * ref_pos, bat * alg_seq, bat * alg_pos, bat *
alg_cigar)
{
@@ -417,7 +416,7 @@ seq_char_bat(bat * ret, int * ref_pos, b
"Misalignment in input BATs: "BUNFMT"/"BUNFMT"/"BUNFMT,
BATcount(poss), BATcount(seqs), BATcount(cigars));
}
-
+
/* allocate result BAT */
result = BATnew(TYPE_void, TYPE_str, BATcount(cigars), TRANSIENT);
if (result == NULL) {
@@ -450,7 +449,7 @@ seq_char_bat(bat * ret, int * ref_pos, b
++pos;
++cigar;
}
-
+
/* release input BAT-descriptors */
BBPreleaseref(seqs->batCacheid);
BBPreleaseref(poss->batCacheid);
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