[med-svn] [htslib] 10/10: Replaced the CRAM-specific verbosity flag with the regular log level setting.
Andreas Tille
tille at debian.org
Wed Jul 19 19:54:43 UTC 2017
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tille pushed a commit to branch master
in repository htslib.
commit cc55632993313cf4c23be82f8b13f7113d61e675
Author: Anders Kaplan <anders.kaplan at magasin1.se>
Date: Mon Jul 3 22:45:12 2017 +0200
Replaced the CRAM-specific verbosity flag with the regular log level setting.
---
cram/cram_encode.c | 19 +++++++------------
cram/cram_io.c | 21 +++++++--------------
cram/cram_structs.h | 1 -
htslib/hts.h | 2 +-
4 files changed, 15 insertions(+), 28 deletions(-)
diff --git a/cram/cram_encode.c b/cram/cram_encode.c
index 2d78732..2b06b58 100644
--- a/cram/cram_encode.c
+++ b/cram/cram_encode.c
@@ -499,9 +499,7 @@ cram_block *cram_encode_compression_header(cram_fd *fd, cram_container *c,
itf8_put_blk(cb, mc);
BLOCK_APPEND(cb, BLOCK_DATA(map), BLOCK_SIZE(map));
- if (fd->verbose)
- hts_log_info("Wrote compression block header in %d bytes",
- (int)BLOCK_SIZE(cb));
+ hts_log_info("Wrote compression block header in %d bytes", (int)BLOCK_SIZE(cb));
BLOCK_UPLEN(cb);
@@ -1405,8 +1403,7 @@ int cram_encode_container(cram_fd *fd, cram_container *c) {
multi_ref = c->stats[DS_RI]->nvals > 1;
if (multi_ref) {
- if (fd->verbose)
- hts_log_info("Multi-ref container");
+ hts_log_info("Multi-ref container");
c->ref_seq_id = -2;
c->ref_seq_start = 0;
c->ref_seq_span = 0;
@@ -1640,8 +1637,7 @@ int cram_encode_container(cram_fd *fd, cram_container *c) {
/* Encode slices */
for (i = 0; i < c->curr_slice; i++) {
- if (fd->verbose)
- hts_log_info("Encode slice %d", i);
+ hts_log_info("Encode slice %d", i);
if (cram_encode_slice(fd, c, h, c->slices[i]) != 0)
return -1;
@@ -2445,10 +2441,9 @@ static cram_container *cram_next_container(cram_fd *fd, bam_seq_t *b) {
if (c->curr_slice == c->max_slice ||
(bam_ref(b) != c->curr_ref && !c->multi_seq)) {
c->ref_seq_span = fd->last_base - c->ref_seq_start + 1;
- if (fd->verbose)
- hts_log_info("Flush container %d/%d..%d",
- c->ref_seq_id, c->ref_seq_start,
- c->ref_seq_start + c->ref_seq_span -1);
+ hts_log_info("Flush container %d/%d..%d",
+ c->ref_seq_id, c->ref_seq_start,
+ c->ref_seq_start + c->ref_seq_span -1);
/* Encode slices */
if (fd->pool) {
@@ -3085,7 +3080,7 @@ int cram_put_bam_seq(cram_fd *fd, bam_seq_t *b) {
if (fd->multi_seq == -1 && c->curr_rec < c->max_rec/4+10 &&
fd->last_slice && fd->last_slice < c->max_rec/4+10 &&
!fd->embed_ref) {
- if (fd->verbose && !c->multi_seq)
+ if (!c->multi_seq)
hts_log_info("Multi-ref enabled for this container");
multi_seq = 1;
}
diff --git a/cram/cram_io.c b/cram/cram_io.c
index bf50130..0a88714 100644
--- a/cram/cram_io.c
+++ b/cram/cram_io.c
@@ -1411,10 +1411,9 @@ int cram_compress_block(cram_fd *fd, cram_block *b, cram_metrics *metrics,
b->method = GZIP;
}
- if (fd->verbose)
- hts_log_info("Compressed block ID %d from %d to %d by method %s",
- b->content_id, b->uncomp_size, b->comp_size,
- cram_block_method2str(b->method));
+ hts_log_info("Compressed block ID %d from %d to %d by method %s",
+ b->content_id, b->uncomp_size, b->comp_size,
+ cram_block_method2str(b->method));
if (b->method == RANS1)
b->method = RANS0; // Spec just has RANS (not 0/1) with auto-sensing
@@ -2021,8 +2020,7 @@ static int cram_populate_ref(cram_fd *fd, int id, ref_entry *r) {
mFILE *mf;
int local_path = 0;
- if (fd->verbose)
- hts_log_info("Running cram_populate_ref on fd %p, id %d", (void *)fd, id);
+ hts_log_info("Running cram_populate_ref on fd %p, id %d", (void *)fd, id);
cache_root[0] = '\0';
@@ -2038,8 +2036,7 @@ static int cram_populate_ref(cram_fd *fd, int id, ref_entry *r) {
snprintf(cache_root, PATH_MAX, "%s%s/hts-ref", base, extra);
snprintf(cache,PATH_MAX, "%s%s/hts-ref/%%2s/%%2s/%%s", base, extra);
local_cache = cache;
- if (fd->verbose)
- hts_log_info("Populating local cache: %s", local_cache);
+ hts_log_info("Populating local cache: %s", local_cache);
}
}
@@ -2052,8 +2049,7 @@ static int cram_populate_ref(cram_fd *fd, int id, ref_entry *r) {
if (!(tag = sam_hdr_find_key(fd->header, ty, "M5", NULL)))
goto no_M5;
- if (fd->verbose)
- hts_log_info("Querying ref %s", tag->str+3);
+ hts_log_info("Querying ref %s", tag->str+3);
/* Use cache if available */
if (local_cache && *local_cache) {
@@ -2164,8 +2160,7 @@ static int cram_populate_ref(cram_fd *fd, int id, ref_entry *r) {
}
expand_cache_path(path, local_cache, tag->str+3);
- if (fd->verbose)
- hts_log_info("Writing cache file '%s'", path);
+ hts_log_info("Writing cache file '%s'", path);
mkdir_prefix(path, 01777);
do {
@@ -4072,7 +4067,6 @@ cram_fd *cram_dopen(hFILE *fp, const char *filename, const char *mode) {
fd->ref = NULL;
fd->decode_md = 0;
- fd->verbose = 0;
fd->seqs_per_slice = SEQS_PER_SLICE;
fd->bases_per_slice = BASES_PER_SLICE;
fd->slices_per_container = SLICE_PER_CNT;
@@ -4340,7 +4334,6 @@ int cram_set_voption(cram_fd *fd, enum hts_fmt_option opt, va_list args) {
break;
case CRAM_OPT_VERBOSITY:
- fd->verbose = va_arg(args, int);
break;
case CRAM_OPT_SEQS_PER_SLICE:
diff --git a/cram/cram_structs.h b/cram/cram_structs.h
index eeba679..a50507e 100644
--- a/cram/cram_structs.h
+++ b/cram/cram_structs.h
@@ -706,7 +706,6 @@ typedef struct cram_fd {
// options
int decode_md; // Whether to export MD and NM tags
- int verbose;
int seqs_per_slice;
int bases_per_slice;
int slices_per_container;
diff --git a/htslib/hts.h b/htslib/hts.h
index e67a80b..75353f1 100644
--- a/htslib/hts.h
+++ b/htslib/hts.h
@@ -210,7 +210,7 @@ enum hts_fmt_option {
// CRAM specific
CRAM_OPT_DECODE_MD,
CRAM_OPT_PREFIX,
- CRAM_OPT_VERBOSITY, // make general
+ CRAM_OPT_VERBOSITY, // obsolete, use hts_set_log_level() instead
CRAM_OPT_SEQS_PER_SLICE,
CRAM_OPT_SLICES_PER_CONTAINER,
CRAM_OPT_RANGE,
--
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