-Wstrict-prototypes

README.md

@@ -41,13 +41,13 @@ depend on your connection to the servers.
 
 ## Read VCF as tabular data in R
 
-This example shows how to read only SNP variants with FILTER=“PASS” and
-GT format in the VCF/BCF into R tables:
+This example shows how to read only SNP variants with genotypes in the
+VCF/BCF into R tables:
 
 ``` r
 library(vcfppR)
 vcffile <- "https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/1kGP_high_coverage_Illumina.chr21.filtered.SNV_INDEL_SV_phased_panel.vcf.gz"
-res <- vcftable(vcffile, "chr21:1-5100000", vartype = "snps", pass = TRUE)
+res <- vcftable(vcffile, "chr21:1-5100000", vartype = "snps")
 str(res)
 ```
 

src/htslib-1.18/Makefile.vcfppR

@@ -38,7 +38,7 @@ CPPFLAGS =
 # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
 # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
 #CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600
-CFLAGS   += -fpic -fvisibility=hidden
+CFLAGS   += -fpic -fvisibility=hidden -Wstrict-prototypes
 EXTRA_CFLAGS_PIC = 
 TARGET_CFLAGS =
 LDFLAGS  += -fvisibility=hidden

src/htslib-1.18/Makefile.win

@@ -41,7 +41,7 @@ CPPFLAGS += -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB
 # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
 # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
 #CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600
-CFLAGS += -fpic -fvisibility=hidden
+CFLAGS += -fpic -fvisibility=hidden -Wstrict-prototypes 
 EXTRA_CFLAGS_PIC =
 TARGET_CFLAGS =
 LDFLAGS  = -fvisibility=hidden

src/htslib-1.18/header.c

@@ -2295,7 +2295,7 @@ void sam_hdr_incr_ref(sam_hdr_t *bh) {
  * Returns a sam_hrecs_t struct on success (free with sam_hrecs_free())
  *         NULL on failure
  */
-sam_hrecs_t *sam_hrecs_new() {
+sam_hrecs_t *sam_hrecs_new(void) {
     sam_hrecs_t *hrecs = calloc(1, sizeof(*hrecs));
 
     if (!hrecs)

src/htslib-1.18/hfile.c

@@ -955,7 +955,7 @@ void hfile_shutdown(int do_close_plugin)
     pthread_mutex_unlock(&plugins_lock);
 }
 
-static void hfile_exit()
+static void hfile_exit(void)
 {
     hfile_shutdown(0);
     pthread_mutex_destroy(&plugins_lock);
@@ -1057,7 +1057,7 @@ static int init_add_plugin(void *obj, int (*init)(struct hFILE_plugin *),
  * Returns 0 on success,
  *        <0 on failure
  */
-static int load_hfile_plugins()
+static int load_hfile_plugins(void)
 {
     static const struct hFILE_scheme_handler
         data = { hopen_mem, hfile_always_local, "built-in", 80 },

src/htslib-1.18/hfile_libcurl.c

@@ -277,7 +277,7 @@ static void free_auth(auth_token *tok) {
     free(tok);
 }
 
-static void libcurl_exit()
+static void libcurl_exit(void)
 {
     if (curl_share_cleanup(curl.share) == CURLSHE_OK)
         curl.share = NULL;

src/htslib-1.18/hts.c

@@ -81,7 +81,7 @@ KHASH_INIT2(s2i,, kh_cstr_t, int64_t, 1, kh_str_hash_func, kh_str_hash_equal)
 HTSLIB_EXPORT
 int hts_verbose = HTS_LOG_WARNING;
 
-const char *hts_version()
+const char *hts_version(void)
 {
     return HTS_VERSION_TEXT;
 }
@@ -4900,7 +4900,7 @@ int hts_resize_array_(size_t item_size, size_t num, size_t size_sz,
     return 0;
 }
 
-void hts_lib_shutdown()
+void hts_lib_shutdown(void)
 {
     hfile_shutdown(1);
 }
@@ -4914,7 +4914,7 @@ void hts_set_log_level(enum htsLogLevel level)
     hts_verbose = level;
 }
 
-enum htsLogLevel hts_get_log_level()
+enum htsLogLevel hts_get_log_level(void)
 {
     return hts_verbose;
 }

src/htslib-1.18/htscodecs/htscodecs/htscodecs.c

@@ -39,6 +39,6 @@
  * NB: This is obtained from the auto-generated version.h, so
  * we can include release number and git hash.
  */
-const char *htscodecs_version() {
+const char *htscodecs_version(void) {
     return HTSCODECS_VERSION_TEXT;
 }

src/htslib-1.18/htscodecs/htscodecs/htscodecs.h

@@ -50,6 +50,6 @@
  * NB: This is obtained from the auto-generated version.h, so
  * we can include release number and git hash.
  */
-const char *htscodecs_version();
+const char *htscodecs_version(void);
 
 #endif /* HTSCODECS_H */

src/htslib-1.18/sam.c

@@ -100,7 +100,7 @@ const int8_t bam_cigar_table[256] = {
     -1, -1, -1, -1,  -1, -1, -1, -1,  -1, -1, -1, -1,  -1, -1, -1, -1
 };
 
-sam_hdr_t *sam_hdr_init()
+sam_hdr_t *sam_hdr_init(void)
 {
     sam_hdr_t *bh = (sam_hdr_t*)calloc(1, sizeof(sam_hdr_t));
     if (bh == NULL) return NULL;
@@ -410,7 +410,7 @@ const char *sam_parse_region(sam_hdr_t *h, const char *s, int *tid,
  *** BAM alignment I/O ***
  *************************/
 
-bam1_t *bam_init1()
+bam1_t *bam_init1(void)
 {
     return (bam1_t*)calloc(1, sizeof(bam1_t));
 }

src/htslib-1.18/textutils.c

@@ -220,7 +220,7 @@ static char token_type(hts_json_token *token)
 }
 
 HTSLIB_EXPORT
-hts_json_token * hts_json_alloc_token() {
+hts_json_token * hts_json_alloc_token(void) {
     return calloc(1, sizeof(hts_json_token));
 }
 

src/htslib-1.18/vcf.c

@@ -1519,7 +1519,7 @@ int bcf_hdr_write(htsFile *hfp, bcf_hdr_t *h)
  *** BCF site I/O ***
  ********************/
 
-bcf1_t *bcf_init()
+bcf1_t *bcf_init(void)
 {
     bcf1_t *v;
     v = (bcf1_t*)calloc(1, sizeof(bcf1_t));