Changeset: f65133aa1630 for MonetDB
URL: https://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=f65133aa1630
Modified Files:
sql/backends/monet5/vaults/bam/bam_wrapper.c
Branch: default
Log Message:
Merge with Jul2017 branch.
diffs (34 lines):
diff --git a/sql/backends/monet5/vaults/bam/bam_wrapper.c
b/sql/backends/monet5/vaults/bam/bam_wrapper.c
--- a/sql/backends/monet5/vaults/bam/bam_wrapper.c
+++ b/sql/backends/monet5/vaults/bam/bam_wrapper.c
@@ -159,7 +159,11 @@ init_bam_wrapper(bam_wrapper * bw, filet
throw(MAL, "init_bam_wrapper", SQLSTATE(HY001)
MAL_MALLOC_FAIL);
}
while (TRUE) {
- int read = mnstr_readline(bw->sam.input, bw->sam.header
+ header_len, bufsize - header_len);
+ ssize_t read;
+ lng header_pos;
+
+ mnstr_fgetpos(bw->sam.input, &header_pos);
+ read = mnstr_readline(bw->sam.input, bw->sam.header +
header_len, bufsize - header_len);
if (read <= 0) {
throw(MAL, "init_bam_wrapper",
@@ -170,7 +174,7 @@ init_bam_wrapper(bam_wrapper * bw, filet
if (bw->sam.header[header_len] != '@') {
/* This is not a header line, we assume that
the header is finished.
* Rewind stream to start of line and stop
reading */
- if (mnstr_fsetpos(bw->sam.input, header_len) <
0) {
+ if (mnstr_fsetpos(bw->sam.input, header_pos) <
0) {
throw(MAL, "init_bam_wrapper",
ERR_INIT_BAM_WRAPPER "Could not read
last line of SAM header",
file_location);
@@ -188,7 +192,7 @@ init_bam_wrapper(bam_wrapper * bw, filet
throw(MAL, "init_bam_wrapper",
SQLSTATE(HY001) MAL_MALLOC_FAIL);
}
bw->sam.header = tmp;
- if (mnstr_fsetpos(bw->sam.input, header_len) <
0) {
+ if (mnstr_fsetpos(bw->sam.input, header_pos) <
0) {
throw(MAL, "init_bam_wrapper",
ERR_INIT_BAM_WRAPPER "Could not read
last line of SAM header",
file_location);
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