This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository htslib.
commit cc55632993313cf4c23be82f8b13f7113d61e675 Author: Anders Kaplan <[email protected]> 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, -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/htslib.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
