[med-svn] [htslib] 02/10: Replaced fprintf(stderr, ...) calls with hts_log_<level> calls.
Andreas Tille
tille at debian.org
Wed Jul 19 19:54:28 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to annotated tag 1.5
in repository htslib.
commit f0fc3eea33477ed45f5f9ffa34f6fea7365513d8
Author: Anders Kaplan <anders.kaplan at magasin1.se>
Date: Sat Jun 3 22:01:27 2017 +0200
Replaced fprintf(stderr, ...) calls with hts_log_<level> calls.
---
faidx.c | 19 +++++++++----------
hts.c | 8 ++++----
htslib/vcf.h | 2 +-
knetfile.c | 24 ++++++++++++------------
regidx.c | 16 ++++++++--------
sam.c | 14 +++++++-------
synced_bcf_reader.c | 46 ++++++++++++++++++++++++++--------------------
tbx.c | 5 +++--
vcf.c | 10 ++++------
9 files changed, 74 insertions(+), 70 deletions(-)
diff --git a/faidx.c b/faidx.c
index bdd98cb..f85ffb5 100644
--- a/faidx.c
+++ b/faidx.c
@@ -63,7 +63,7 @@ struct __faidx_t {
static inline int fai_insert_index(faidx_t *idx, const char *name, int64_t len, int line_len, int line_blen, uint64_t offset)
{
if (!name) {
- fprintf(stderr, "[fai_build_core] malformed line\n");
+ hts_log_error("Malformed line");
return -1;
}
@@ -73,7 +73,7 @@ static inline int fai_insert_index(faidx_t *idx, const char *name, int64_t len,
faidx1_t *v = &kh_value(idx->hash, k);
if (! absent) {
- fprintf(stderr, "[fai_build_core] ignoring duplicate sequence \"%s\" at byte offset %"PRIu64"\n", name, offset);
+ hts_log_warning("Ignoring duplicate sequence \"%s\" at byte offset %"PRIu64"", name, offset);
free(name_key);
return 0;
}
@@ -82,7 +82,7 @@ static inline int fai_insert_index(faidx_t *idx, const char *name, int64_t len,
char **tmp;
idx->m = idx->m? idx->m<<1 : 16;
if (!(tmp = (char**)realloc(idx->name, sizeof(char*) * idx->m))) {
- fprintf(stderr, "[fai_build_core] out of memory\n");
+ hts_log_error("Out of memory");
return -1;
}
idx->name = tmp;
@@ -130,7 +130,7 @@ faidx_t *fai_build_core(BGZF *bgzf)
kputsn("", 0, &name);
if ( c<0 ) {
- fprintf(stderr, "[fai_build_core] the last entry has no sequence\n");
+ hts_log_error("The last entry has no sequence");
goto fail;
}
if (c != '\n') while ( (c=bgzf_getc(bgzf))>=0 && c != '\n');
@@ -138,7 +138,7 @@ faidx_t *fai_build_core(BGZF *bgzf)
offset = bgzf_utell(bgzf);
} else {
if (state == 3) {
- fprintf(stderr, "[fai_build_core] inlined empty line is not allowed in sequence '%s'.\n", name.s);
+ hts_log_error("Inlined empty line is not allowed in sequence '%s'", name.s);
goto fail;
}
if (state == 2) state = 3;
@@ -148,7 +148,7 @@ faidx_t *fai_build_core(BGZF *bgzf)
if (isgraph(c)) ++l2;
} while ( (c=bgzf_getc(bgzf))>=0 && c != '\n');
if (state == 3 && l2) {
- fprintf(stderr, "[fai_build_core] different line length in sequence '%s'.\n", name.s);
+ hts_log_error("Different line length in sequence '%s'", name.s);
goto fail;
}
++l1; len += l2;
@@ -498,7 +498,7 @@ char *fai_fetch(const faidx_t *fai, const char *str, int *len)
}
} else iter = kh_get(s, h, str);
if(iter == kh_end(h)) {
- fprintf(stderr, "[fai_fetch] Warning - Reference %s not found in FASTA file, returning empty sequence\n", str);
+ hts_log_warning("Reference %s not found in FASTA file, returning empty sequence", str);
free(s);
*len = -2;
return 0;
@@ -523,8 +523,7 @@ char *fai_fetch(const faidx_t *fai, const char *str, int *len)
// Check for out of range numbers. Only going to be a problem on
// 32-bit platforms with >2Gb sequence length.
if (errno == ERANGE && (uint64_t) val.len > LONG_MAX) {
- fprintf(stderr, "[fai_fetch] Positions in range %s are too large"
- " for this platform.\n", s);
+ hts_log_error("Positions in range %s are too large for this platform", s);
free(s);
*len = -2;
return NULL;
@@ -572,7 +571,7 @@ char *faidx_fetch_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p
if (iter == kh_end(fai->hash))
{
*len = -2;
- fprintf(stderr, "[fai_fetch_seq] The sequence \"%s\" not found\n", c_name);
+ hts_log_error("The sequence \"%s\" not found", c_name);
return NULL;
}
val = kh_value(fai->hash, iter);
diff --git a/hts.c b/hts.c
index 2736456..355d51d 100644
--- a/hts.c
+++ b/hts.c
@@ -568,7 +568,7 @@ int hts_opt_add(hts_opt **opts, const char *c_arg) {
case 'k': case 'K': o->val.i *= 1024; break;
case '\0': break;
default:
- fprintf(stderr, "Unrecognised cache size suffix '%c'\n", *endp);
+ hts_log_error("Unrecognised cache size suffix '%c'", *endp);
free(o->arg);
free(o);
return -1;
@@ -588,7 +588,7 @@ int hts_opt_add(hts_opt **opts, const char *c_arg) {
o->opt = CRAM_OPT_PREFIX, o->val.s = val;
else {
- fprintf(stderr, "Unknown option '%s'\n", o->arg);
+ hts_log_error("Unknown option '%s'", o->arg);
free(o->arg);
free(o);
return -1;
@@ -902,7 +902,7 @@ int hts_close(htsFile *fp)
if (!fp->is_write) {
switch (cram_eof(fp->fp.cram)) {
case 2:
- fprintf(stderr, "[W::%s] EOF marker is absent. The input is probably truncated.\n", __func__);
+ hts_log_warning("EOF marker is absent. The input is probably truncated");
break;
case 0: /* not at EOF, but may not have wanted all seqs */
default: /* case 1, expected EOF */
@@ -1072,7 +1072,7 @@ int hts_getline(htsFile *fp, int delimiter, kstring_t *str)
{
int ret;
if (! (delimiter == KS_SEP_LINE || delimiter == '\n')) {
- fprintf(stderr, "[hts_getline] unexpected delimiter %d\n", delimiter);
+ hts_log_error("Unexpected delimiter %d", delimiter);
abort();
}
diff --git a/htslib/vcf.h b/htslib/vcf.h
index 55d6b3b..4ee8739 100644
--- a/htslib/vcf.h
+++ b/htslib/vcf.h
@@ -914,7 +914,7 @@ static inline void bcf_format_gt(bcf_fmt_t *fmt, int isample, kstring_t *str)
case BCF_BT_INT16: BRANCH(int16_t, bcf_int16_missing, bcf_int16_vector_end); break;
case BCF_BT_INT32: BRANCH(int32_t, bcf_int32_missing, bcf_int32_vector_end); break;
case BCF_BT_NULL: kputc('.', str); break;
- default: fprintf(stderr,"FIXME: type %d in bcf_format_gt?\n", fmt->type); abort(); break;
+ default: hts_log_error("Unexpected type %d", fmt->type); abort(); break;
}
#undef BRANCH
}
diff --git a/knetfile.c b/knetfile.c
index 9e8af13..dc20782 100644
--- a/knetfile.c
+++ b/knetfile.c
@@ -76,9 +76,9 @@ static int socket_wait(int fd, int is_read)
if (ret == -1) perror("select");
#else
if (ret == 0)
- fprintf(stderr, "select time-out\n");
+ hts_log_warning("Select timed out");
else if (ret == SOCKET_ERROR)
- fprintf(stderr, "select: %d\n", WSAGetLastError());
+ hts_log_error("Select returned error %d", WSAGetLastError());
#endif
return ret;
}
@@ -99,7 +99,7 @@ static int socket_connect(const char *host, const char *port)
hints.ai_socktype = SOCK_STREAM;
/* In Unix/Mac, getaddrinfo() is the most convenient way to get
* server information. */
- if ((ai_err = getaddrinfo(host, port, &hints, &res)) != 0) { fprintf(stderr, "can't resolve %s:%s: %s\n", host, port, gai_strerror(ai_err)); return -1; }
+ if ((ai_err = getaddrinfo(host, port, &hints, &res)) != 0) { hts_log_error("Can't resolve %s:%s: %s", host, port, gai_strerror(ai_err)); return -1; }
if ((fd = socket(res->ai_family, res->ai_socktype, res->ai_protocol)) == -1) __err_connect("socket");
/* The following two setsockopt() are used by ftplib
* (http://nbpfaus.net/~pfau/ftplib/). I am not sure if they
@@ -150,10 +150,10 @@ void knet_win32_destroy()
* non-Windows OS, I do not use this one. */
static SOCKET socket_connect(const char *host, const char *port)
{
-#define __err_connect(func) \
- do { \
- fprintf(stderr, "%s: %d\n", func, WSAGetLastError()); \
- return -1; \
+#define __err_connect(func) \
+ do { \
+ hts_log_error("The %s operation returned error %d", func, WSAGetLastError()); \
+ return -1; \
} while (0)
int on = 1;
@@ -261,7 +261,7 @@ static int kftp_pasv_connect(knetFile *ftp)
{
char host[80], port[10];
if (ftp->pasv_port == 0) {
- fprintf(stderr, "[kftp_pasv_connect] kftp_pasv_prep() is not called before hand.\n");
+ hts_log_error("Must call kftp_pasv_prep() first");
return -1;
}
sprintf(host, "%d.%d.%d.%d", ftp->pasv_ip[0], ftp->pasv_ip[1], ftp->pasv_ip[2], ftp->pasv_ip[3]);
@@ -356,7 +356,7 @@ int kftp_connect_file(knetFile *fp)
kftp_pasv_connect(fp);
ret = kftp_get_response(fp);
if (ret != 150) {
- fprintf(stderr, "[kftp_connect_file] %s\n", fp->response);
+ hts_log_error("%s", fp->response);
netclose(fp->fd);
fp->fd = -1;
return -1;
@@ -467,7 +467,7 @@ knetFile *knet_open(const char *fn, const char *mode)
{
knetFile *fp = 0;
if (mode[0] != 'r') {
- fprintf(stderr, "[knet_open] only mode \"r\" is supported.\n");
+ hts_log_error("Only mode \"r\" is supported");
errno = ENOTSUP;
return 0;
}
@@ -563,7 +563,7 @@ off_t knet_seek(knetFile *fp, off_t off, int whence)
return fp->offset;
} else if (fp->type == KNF_TYPE_HTTP) {
if (whence == SEEK_END) { // FIXME: can we allow SEEK_END in future?
- fprintf(stderr, "[knet_seek] SEEK_END is not supported for HTTP. Offset is unchanged.\n");
+ hts_log_error("SEEK_END is not supported for HTTP. Offset is unchanged");
errno = ESPIPE;
return -1;
}
@@ -574,7 +574,7 @@ off_t knet_seek(knetFile *fp, off_t off, int whence)
return fp->offset;
}
errno = EINVAL;
- fprintf(stderr,"[knet_seek] %s\n", strerror(errno));
+ hts_log_error("%s", strerror(errno));
return -1;
}
diff --git a/regidx.c b/regidx.c
index 68f92c4..5c4c77d 100644
--- a/regidx.c
+++ b/regidx.c
@@ -154,9 +154,9 @@ int regidx_insert(regidx_t *idx, char *line)
if ( idx->rid_prev==rid )
{
if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) )
- {
- fprintf(stderr,"The regions are not sorted: %s:%d-%d is before %s:%d-%d\n",
- idx->str.s,idx->start_prev+1,idx->end_prev+1,idx->str.s,reg.start+1,reg.end+1);
+ {
+ hts_log_error("The regions are not sorted: %s:%d-%d is before %s:%d-%d",
+ idx->str.s,idx->start_prev+1,idx->end_prev+1,idx->str.s,reg.start+1,reg.end+1);
return -1;
}
}
@@ -293,18 +293,18 @@ int regidx_parse_bed(const char *line, char **chr_beg, char **chr_end, reg_t *re
char *se = ss;
while ( *se && !isspace_c(*se) ) se++;
- if ( !*se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
+ if ( !*se ) { hts_log_error("Could not parse bed line: %s", line); return -2; }
*chr_beg = ss;
*chr_end = se-1;
ss = se+1;
reg->start = hts_parse_decimal(ss, &se, 0);
- if ( ss==se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
+ if ( ss==se ) { hts_log_error("Could not parse bed line: %s", line); return -2; }
ss = se+1;
reg->end = hts_parse_decimal(ss, &se, 0) - 1;
- if ( ss==se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
+ if ( ss==se ) { hts_log_error("Could not parse bed line: %s", line); return -2; }
return 0;
}
@@ -318,14 +318,14 @@ int regidx_parse_tab(const char *line, char **chr_beg, char **chr_end, reg_t *re
char *se = ss;
while ( *se && !isspace_c(*se) ) se++;
- if ( !*se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
+ if ( !*se ) { hts_log_error("Could not parse bed line: %s", line); return -2; }
*chr_beg = ss;
*chr_end = se-1;
ss = se+1;
reg->start = hts_parse_decimal(ss, &se, 0) - 1;
- if ( ss==se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
+ if ( ss==se ) { hts_log_error("Could not parse bed line: %s", line); return -2; }
if ( !se[0] || !se[1] )
reg->end = reg->start;
diff --git a/sam.c b/sam.c
index a18168a..5e9c20d 100644
--- a/sam.c
+++ b/sam.c
@@ -578,7 +578,7 @@ static int sam_bam_cram_readrec(BGZF *bgzfp, void *fpv, void *bv, int *tid, int
case cram: return cram_get_bam_seq(fp->fp.cram, &b);
default:
// TODO Need headers available to implement this for SAM files
- fprintf(stderr, "[sam_bam_cram_readrec] Not implemented for SAM files -- Exiting\n");
+ hts_log_error("Not implemented for SAM files");
abort();
}
}
@@ -658,7 +658,7 @@ static hts_itr_t *cram_itr_query(const hts_idx_t *idx, int tid, int beg, int end
iter->finished = 1;
break;
default:
- fprintf(stderr, "[cram_itr_query] tid=%d not implemented for CRAM files -- Exiting\n", tid);
+ hts_log_error("Query with tid=%d not implemented for CRAM files", tid);
abort();
break;
}
@@ -2035,7 +2035,7 @@ static inline int cigar_iref2iseq_set(uint32_t **cigar, uint32_t *cigar_max, int
(*cigar)++; *icig = 0; *iref += ncig;
continue;
}
- fprintf(stderr,"todo: cigar %d\n", cig);
+ hts_log_error("Unexpected cigar %d", cig);
assert(0);
}
*iseq = -1;
@@ -2058,7 +2058,7 @@ static inline int cigar_iref2iseq_next(uint32_t **cigar, uint32_t *cigar_max, in
if ( cig==BAM_CINS ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; }
if ( cig==BAM_CSOFT_CLIP ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; }
if ( cig==BAM_CHARD_CLIP || cig==BAM_CPAD ) { (*cigar)++; *icig = 0; continue; }
- fprintf(stderr,"todo: cigar %d\n", cig);
+ hts_log_error("Unexpected cigar %d", cig);
assert(0);
}
*iseq = -1;
@@ -2228,7 +2228,7 @@ const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_
// update iter->tid and iter->pos
if (iter->head != iter->tail) {
if (iter->tid > iter->head->b.core.tid) {
- fprintf(stderr, "[%s] unsorted input. Pileup aborts.\n", __func__);
+ hts_log_error("Unsorted input. Pileup aborts");
iter->error = 1;
*_n_plp = -1;
return NULL;
@@ -2267,12 +2267,12 @@ int bam_plp_push(bam_plp_t iter, const bam1_t *b)
iter->tail->end = bam_endpos(b);
iter->tail->s = g_cstate_null; iter->tail->s.end = iter->tail->end - 1; // initialize cstate_t
if (b->core.tid < iter->max_tid) {
- fprintf(stderr, "[bam_pileup_core] the input is not sorted (chromosomes out of order)\n");
+ hts_log_error("The input is not sorted (chromosomes out of order)");
iter->error = 1;
return -1;
}
if ((b->core.tid == iter->max_tid) && (iter->tail->beg < iter->max_pos)) {
- fprintf(stderr, "[bam_pileup_core] the input is not sorted (reads out of order)\n");
+ hts_log_error("The input is not sorted (reads out of order)");
iter->error = 1;
return -1;
}
diff --git a/synced_bcf_reader.c b/synced_bcf_reader.c
index 9c2de9d..47715da 100644
--- a/synced_bcf_reader.c
+++ b/synced_bcf_reader.c
@@ -149,7 +149,7 @@ int bcf_sr_set_regions(bcf_srs_t *readers, const char *regions, int is_file)
assert( !readers->regions );
if ( readers->nreaders )
{
- fprintf(stderr,"[%s:%d %s] Error: bcf_sr_set_regions() must be called before bcf_sr_add_reader()\n", __FILE__,__LINE__,__FUNCTION__);
+ hts_log_error("Must call bcf_sr_set_regions() before bcf_sr_add_reader()");
return -1;
}
readers->regions = bcf_sr_regions_init(regions,is_file,0,1,-2);
@@ -220,7 +220,7 @@ int bcf_sr_add_reader(bcf_srs_t *files, const char *fname)
BGZF *bgzf = hts_get_bgzfp(reader->file);
if ( bgzf && bgzf_check_EOF(bgzf) == 0 ) {
files->errnum = no_eof;
- fprintf(stderr,"[%s] Warning: no BGZF EOF marker; file may be truncated.\n", fname);
+ hts_log_warning("No BGZF EOF marker; file '%s' may be truncated", fname);
}
if (files->p)
bgzf_thread_pool(bgzf, files->p->pool, files->p->qsize);
@@ -284,13 +284,13 @@ int bcf_sr_add_reader(bcf_srs_t *files, const char *fname)
if ( files->streaming && files->nreaders>1 )
{
files->errnum = api_usage_error;
- fprintf(stderr,"[%s:%d %s] Error: %d readers, yet require_index not set\n", __FILE__,__LINE__,__FUNCTION__,files->nreaders);
+ hts_log_error("Must set require_index when the number of readers is greater than one");
return 0;
}
if ( files->streaming && files->regions )
{
files->errnum = api_usage_error;
- fprintf(stderr,"[%s:%d %s] Error: cannot tabix-jump in streaming mode\n", __FILE__,__LINE__,__FUNCTION__);
+ hts_log_error("Cannot tabix-jump in streaming mode");
return 0;
}
if ( !reader->header )
@@ -422,7 +422,7 @@ static int _reader_seek(bcf_sr_t *reader, const char *seq, int start, int end)
{
if ( end>=MAX_CSI_COOR )
{
- fprintf(stderr,"The coordinate is out of csi index limit: %d\n", end+1);
+ hts_log_error("The coordinate is out of csi index limit: %d", end+1);
exit(1);
}
if ( reader->itr )
@@ -443,8 +443,10 @@ static int _reader_seek(bcf_sr_t *reader, const char *seq, int start, int end)
if ( tid==-1 ) return -1; // the sequence not present in this file
reader->itr = bcf_itr_queryi(reader->bcf_idx,tid,start,end+1);
}
- if ( !reader->itr ) fprintf(stderr,"Could not seek: %s:%d-%d\n",seq,start+1,end+1);
- assert(reader->itr);
+ if (!reader->itr) {
+ hts_log_error("Could not seek: %s:%d-%d", seq, start + 1, end + 1);
+ assert(0);
+ }
return 0;
}
@@ -517,7 +519,7 @@ static void _reader_fill_buffer(bcf_srs_t *files, bcf_sr_t *reader)
}
else
{
- fprintf(stderr,"[%s:%d %s] fixme: not ready for this\n", __FILE__,__LINE__,__FUNCTION__);
+ hts_log_error("Fixme: not ready for this");
exit(1);
}
}
@@ -693,7 +695,7 @@ int bcf_sr_set_samples(bcf_srs_t *files, const char *fname, int is_file)
smpl = hts_readlist(fname, is_file, &nsmpl);
if ( !smpl )
{
- fprintf(stderr,"Could not read the file: \"%s\"\n", fname);
+ hts_log_error("Could not read the file: \"%s\"", fname);
return 0;
}
if ( exclude )
@@ -723,7 +725,8 @@ int bcf_sr_set_samples(bcf_srs_t *files, const char *fname, int is_file)
}
if ( n_isec!=files->nreaders )
{
- fprintf(stderr,"Warning: The sample \"%s\" was not found in %s, skipping\n", smpl[i], files->readers[n_isec].fname);
+ hts_log_warning("The sample \"%s\" was not found in %s, skipping",
+ smpl[i], files->readers[n_isec].fname);
continue;
}
@@ -741,7 +744,7 @@ int bcf_sr_set_samples(bcf_srs_t *files, const char *fname, int is_file)
if ( !files->n_smpl )
{
if ( files->nreaders>1 )
- fprintf(stderr,"No samples in common.\n");
+ hts_log_warning("No samples in common");
return 0;
}
for (i=0; i<files->nreaders; i++)
@@ -828,7 +831,7 @@ static bcf_sr_regions_t *_regions_init_string(const char *str)
from = hts_parse_decimal(sp,(char**)&ep,0);
if ( sp==ep )
{
- fprintf(stderr,"[%s:%d %s] Could not parse the region(s): %s\n", __FILE__,__LINE__,__FUNCTION__,str);
+ hts_log_error("Could not parse the region(s): %s", str);
free(reg); free(tmp.s); return NULL;
}
if ( !*ep || *ep==',' )
@@ -839,7 +842,7 @@ static bcf_sr_regions_t *_regions_init_string(const char *str)
}
if ( *ep!='-' )
{
- fprintf(stderr,"[%s:%d %s] Could not parse the region(s): %s\n", __FILE__,__LINE__,__FUNCTION__,str);
+ hts_log_error("Could not parse the region(s): %s", str);
free(reg); free(tmp.s); return NULL;
}
ep++;
@@ -847,7 +850,7 @@ static bcf_sr_regions_t *_regions_init_string(const char *str)
to = hts_parse_decimal(sp,(char**)&ep,0);
if ( *ep && *ep!=',' )
{
- fprintf(stderr,"[%s:%d %s] Could not parse the region(s): %s\n", __FILE__,__LINE__,__FUNCTION__,str);
+ hts_log_error("Could not parse the region(s): %s", str);
free(reg); free(tmp.s); return NULL;
}
if ( sp==ep ) to = MAX_CSI_COOR-1;
@@ -939,7 +942,7 @@ bcf_sr_regions_t *bcf_sr_regions_init(const char *regions, int is_file, int ichr
reg->file = hts_open(regions, "rb");
if ( !reg->file )
{
- fprintf(stderr,"[%s:%d %s] Could not open file: %s\n", __FILE__,__LINE__,__FUNCTION__,regions);
+ hts_log_error("Could not open file: %s", regions);
free(reg);
return NULL;
}
@@ -965,7 +968,8 @@ bcf_sr_regions_t *bcf_sr_regions_init(const char *regions, int is_file, int ichr
ret = _regions_parse_line(reg->line.s, ichr,ifrom,ifrom, &chr,&chr_end,&from,&to);
if ( ret<0 )
{
- fprintf(stderr,"[%s:%d] Could not parse the file %s, using the columns %d,%d[,%d]\n", __FILE__,__LINE__,regions,ichr+1,ifrom+1,ito+1);
+ hts_log_error("Could not parse the file %s, using the columns %d,%d[,%d]",
+ regions,ichr+1,ifrom+1,ito+1);
hts_close(reg->file); reg->file = NULL; free(reg);
return NULL;
}
@@ -1092,7 +1096,7 @@ int bcf_sr_regions_next(bcf_sr_regions_t *reg)
reg->file = hts_open(reg->fname, "r");
if ( !reg->file )
{
- fprintf(stderr,"[%s:%d %s] Could not open file: %s\n", __FILE__,__LINE__,__FUNCTION__,reg->fname);
+ hts_log_error("Could not open file: %s", reg->fname);
reg->file = NULL;
bcf_sr_regions_destroy(reg);
return -1;
@@ -1107,7 +1111,8 @@ int bcf_sr_regions_next(bcf_sr_regions_t *reg)
ret = _regions_parse_line(reg->line.s, ichr,ifrom,ito, &chr,&chr_end,&from,&to);
if ( ret<0 )
{
- fprintf(stderr,"[%s:%d] Could not parse the file %s, using the columns %d,%d,%d\n", __FILE__,__LINE__,reg->fname,ichr+1,ifrom+1,ito+1);
+ hts_log_error("Could not parse the file %s, using the columns %d,%d,%d",
+ reg->fname,ichr+1,ifrom+1,ito+1);
return -1;
}
}
@@ -1116,7 +1121,8 @@ int bcf_sr_regions_next(bcf_sr_regions_t *reg)
*chr_end = 0;
if ( khash_str2int_get(reg->seq_hash, chr, ®->iseq)<0 )
{
- fprintf(stderr,"Broken tabix index? The sequence \"%s\" not in dictionary [%s]\n", chr,reg->line.s);
+ hts_log_error("Broken tabix index? The sequence \"%s\" not in dictionary [%s]",
+ chr, reg->line.s);
exit(1);
}
*chr_end = '\t';
@@ -1131,7 +1137,7 @@ static int _regions_match_alleles(bcf_sr_regions_t *reg, int als_idx, bcf1_t *re
if ( reg->regs )
{
// payload is not supported for in-memory regions, switch to regidx instead in future
- fprintf(stderr,"Error: Compressed and indexed targets file is required\n");
+ hts_log_error("Compressed and indexed targets file is required");
exit(1);
}
diff --git a/tbx.c b/tbx.c
index e92d2d7..1d4b6b5 100644
--- a/tbx.c
+++ b/tbx.c
@@ -158,7 +158,8 @@ static inline int get_intv(tbx_t *tbx, kstring_t *str, tbx_intv_t *intv, int is_
case TBX_UCSC: type = "TBX_UCSC"; break;
default: type = "TBX_GENERIC"; break;
}
- fprintf(stderr, "[E::%s] failed to parse %s, was wrong -p [type] used?\nThe offending line was: \"%s\"\n", __func__, type, str->s);
+ hts_log_error("Failed to parse %s, was wrong -p [type] used?\nThe offending line was: \"%s\"",
+ type, str->s);
return -1;
}
}
@@ -319,7 +320,7 @@ tbx_t *tbx_index_load2(const char *fn, const char *fnidx)
// of whatever it reads.
for (; p - nm < l_nm; p += strlen(p) + 1) {
if (get_tid(tbx, p, 1) < 0) {
- fprintf(stderr, "[E::%s] %s\n", __func__, strerror(errno));
+ hts_log_error("%s", strerror(errno));
goto fail;
}
}
diff --git a/vcf.c b/vcf.c
index 2214dd4..e1f871e 100644
--- a/vcf.c
+++ b/vcf.c
@@ -496,15 +496,13 @@ int bcf_hdr_register_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec)
}
if (hrec->type == BCF_HL_INFO || hrec->type == BCF_HL_FMT) {
if (type == -1) {
- if (hts_verbose >= 2)
- fprintf(stderr, "[E::%s] %s %s field has no Type defined. Assuming String\n",
- __func__, *hrec->key == 'I' ? "An" : "A", hrec->key);
+ hts_log_warning("%s %s field has no Type defined. Assuming String",
+ *hrec->key == 'I' ? "An" : "A", hrec->key);
type = BCF_HT_STR;
}
if (var == -1) {
- if (hts_verbose >= 2)
- fprintf(stderr, "[E::%s] %s %s field has no Number defined. Assuming '.'\n",
- __func__, *hrec->key == 'I' ? "An" : "A", hrec->key);
+ hts_log_warning("%s %s field has no Number defined. Assuming '.'",
+ *hrec->key == 'I' ? "An" : "A", hrec->key);
var = BCF_VL_VAR;
}
}
--
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