Changeset: ffce6d518698 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=ffce6d518698
Modified Files:
sql/backends/monet5/bam/bamloader.c
Branch: DVframework_bam
Log Message:
Fixed bug in parser for alignment strings
diffs (33 lines):
diff --git a/sql/backends/monet5/bam/bamloader.c
b/sql/backends/monet5/bam/bamloader.c
--- a/sql/backends/monet5/bam/bamloader.c
+++ b/sql/backends/monet5/bam/bamloader.c
@@ -761,19 +761,24 @@ str process_bam_alignment(str filepath,
return MAL_SUCCEED;
}
-int parse_alignment_str(str *sam_alig, str *dest)
+static int
+_parse_alignment_str(str *sam_alig, str *dest)
{
- if(read_string_until_delim(sam_alig, dest, "\t", 1) > 0)
+ if(_read_string_until_delim(sam_alig, dest, "\t\n\0", 3) > 0)
{
- while(**sam_alig == '\t') (*sam_alig)++;
+ /* At this moment we're looking at either a tab or one of \n\0. We
just want to skip tabs. \n or \0 however,
+ indicate the end of this alignment, so we want to keep them. In
case we didn't finish all mandatory fields
+ in the alignment yet, the next call to this function will return
FALSE. */
+ while(**sam_alig == '\t') (*sam_alig)++;
return TRUE;
}
return FALSE;
}
-int parse_alignment_lng(str *sam_alig, lng *dest)
+static int
+_parse_alignment_lng(str *sam_alig, lng *dest)
{
- if(parse_lng(sam_alig, dest))
+ if(_parse_lng(sam_alig, dest))
{
while(**sam_alig == '\t') (*sam_alig)++;
return TRUE;
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