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Remove cram seek ability to do range queries via SEEK_CUR. #1878

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merged 1 commit into from
Jan 27, 2025
Merged

Remove cram seek ability to do range queries via SEEK_CUR. #1878

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4 changes: 1 addition & 3 deletions cram/cram_index.c
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Original file line number Diff line number Diff line change
Expand Up @@ -580,9 +580,7 @@ int cram_seek_to_refpos(cram_fd *fd, cram_range *r) {
// Ideally use an index, so see if we have one.
if ((e = cram_index_query(fd, r->refid, r->start, NULL))) {
if (0 != cram_seek(fd, e->offset, SEEK_SET)) {
if (0 != cram_seek(fd, e->offset - fd->first_container, SEEK_CUR)) {
ret = -1; goto err;
}
ret = -1; goto err;
}
} else {
// Absent from index, but this most likely means it simply has no data.
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19 changes: 1 addition & 18 deletions cram/cram_io.c
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Original file line number Diff line number Diff line change
Expand Up @@ -5440,28 +5440,11 @@ cram_fd *cram_dopen(hFILE *fp, const char *filename, const char *mode) {
* -1 on failure
*/
int cram_seek(cram_fd *fd, off_t offset, int whence) {
char buf[65536];

fd->ooc = 0;

cram_drain_rqueue(fd);

if (hseek(fd->fp, offset, whence) >= 0) {
return 0;
}

if (!(whence == SEEK_CUR && offset >= 0))
return -1;

/* Couldn't fseek, but we're in SEEK_CUR mode so read instead */
while (offset > 0) {
int len = MIN(65536, offset);
if (len != hread(fd->fp, buf, len))
return -1;
offset -= len;
}

return 0;
return hseek(fd->fp, offset, whence) >= 0 ? 0 : -1;
}

/*
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