change links

README.md

@@ -145,7 +145,7 @@ Visit the [man page](https://hasindu2008.github.io/f5c/docs/commands) for all th
 Follow the same steps as in [Nanopolish tutorial](https://nanopolish.readthedocs.io/en/latest/quickstart_call_methylation.html) while replacing `nanopolish` with `f5c`. If you only want to perform a quick test of f5c :
 ```sh
 #download and extract the dataset including sorted alignments
-wget -O f5c_na12878_test.tgz "https://f5c.page.link/f5c_na12878_test"
+wget -O f5c_na12878_test.tgz "https://f5c.bioinf.science/f5c_na12878_test"
 tar xf f5c_na12878_test.tgz
 
 ###### Using S/BLOW5 as input (recommended) ######

scripts/install-vbz.sh

@@ -21,7 +21,7 @@ print() {
     echo -e "${GREEN}$1${NC}" >&2
 }
 
-MANUAL_LINK="https://f5c.page.link/troubleshoot"
+MANUAL_LINK="https://f5c.bioinf.science/troubleshoot"
 
 uname -o || die "Could not determine the O/S. See ${MANUAL_LINK}"
 uname -m || die "Could not determine the architecture. See ${MANUAL_LINK}"

scripts/test.sh

@@ -21,8 +21,8 @@ else
 fi
 # execution mode (valgrind/gdb/cpu/cuda/echo)
 mode=
-testset_url="https://f5c.page.link/f5c_ecoli_2kb_region_test"
-fallback_url="https://f5c.page.link/f5c_ecoli_2kb_region_test_fallback"
+testset_url="https://f5c.bioinf.science/f5c_ecoli_2kb_region_test"
+fallback_url="https://f5c.bioinf.science/f5c_ecoli_2kb_region_test_fallback"
 
 # download test set given url
 #
@@ -131,17 +131,17 @@ do
 		   bamfile=${testdir}/reads.sorted.bam
 		   ref=${testdir}/humangenome.fa
 		   reads=${testdir}/reads.fastq
-		   testset_url="https://f5c.page.link/f5c_na12878_test"
-		   fallback_url="https://f5c.page.link/f5c_na12878_test_fallback";;
+		   testset_url="https://f5c.bioinf.science/f5c_na12878_test"
+		   fallback_url="https://f5c.bioinf.science/f5c_na12878_test_fallback";;
 		f) testdir=test/hg2_lsk114_reads_1000
 		   reads=${testdir}/PGXX22394_reads_1000_6.4.2_sup.fastq
 		   slow5=${testdir}/PGXX22394_reads_1000.blow5
 		   ref=test/chr22_meth_example/humangenome.fa
 		   bamfile=${testdir}/PGXX22394_reads_1000_6.4.2_sup.bam
-		   testset_url="https://f5c.page.link/hg2_lsk114_reads_1000";;
+		   testset_url="https://f5c.bioinf.science/hg2_lsk114_reads_1000";;
 		K) batchsize="$OPTARG";;
 		B) max_bases="$OPTARG";;
-		d) download_test_set "https://f5c.page.link/f5c_na12878_test" "https://f5c.page.link/f5c_na12878_test_fallback"
+		d) download_test_set "https://f5c.bioinf.science/f5c_na12878_test" "https://f5c.bioinf.science/f5c_na12878_test_fallback"
 		   exit 0;;
 		h) help_msg
 		   exit 0;;

src/error.h

@@ -50,7 +50,7 @@ static inline void malloc_chk(void* ret, const char* func, const char* file,
         "[%s::ERROR]\033[1;31m Failed to allocate memory : "
         "%s.\033[0m\n[%s::DEBUG]\033[1;35m Error occured at %s:%d. Try with a small batchsize (-K and/or -B options),"
         "fewer threads (-t) or skip ultra-long reads (--skip-ultra) to reduce the peak memory."
-        "See https://f5c.page.link/troubleshoot for details.\033[0m\n\n",
+        "See https://f5c.bioinf.science/troubleshoot for details.\033[0m\n\n",
         func, strerror(errno), func, file, line);
     exit(EXIT_FAILURE);
 }

src/fast5lite.h

@@ -294,7 +294,7 @@ static inline int32_t fast5_read_multi_fast5(fast5_file_t fh, signal_t* sig, std
     if (status < 0) {
         free(sig->rawptr);
         if(fast5_is_vbz_compressed(fh, read_id) == 1) {
-            ERROR("%s","The fast5 file is compressed with VBZ but the required plugin is not loaded. See https://f5c.page.link/troubleshoot for instructions.\n");
+            ERROR("%s","The fast5 file is compressed with VBZ but the required plugin is not loaded. See https://f5c.bioinf.science/troubleshoot for instructions.\n");
         }
         WARNING("Failed to read raw data from dataset %s.", signal_path);
         H5Sclose(space);

src/freq.c

@@ -34,7 +34,7 @@ static const char usage[] = "Usage: %s [OPTIONS] -i methcalls.tsv\n"
                             "  -s              split groups\n"
                             "  -h              help\n"
                             "  --version       print version\n"
-                            "\nSee the manual page for details (`man ./docs/f5c.1' or https://f5c.page.link/man).\n"
+                            "\nSee the manual page for details (`man ./docs/f5c.1' or https://f5c.bioinf.science/man).\n"
                             ;
 
 struct site_stats {

src/freq_merge.c

@@ -136,7 +136,7 @@ static const char *MAP_REDUCE_USAGE_MESSAGE =
         "   -o FILE         output file. Write to stdout if not specified\n"
         "   -h              help\n"
         "   --version       print version\n"
-        "\nSee the manual page for details (`man ./docs/f5c.1' or https://f5c.page.link/man)."
+        "\nSee the manual page for details (`man ./docs/f5c.1' or https://f5c.bioinf.science/man)."
         "\n\n"
 ;
 

src/index.c

@@ -76,7 +76,7 @@ static const char *INDEX_USAGE_MESSAGE =
 "  --skip-slow5-idx  do not build the .idx for the slow5 file (useful when a slow5 index is already available)\n"
 "  --verbose INT     verbosity level\n"
 "  --version         print version\n"
-"\nSee the manual page for details (`man ./docs/f5c.1' or https://f5c.page.link/man)."
+"\nSee the manual page for details (`man ./docs/f5c.1' or https://f5c.bioinf.science/man)."
 "\n\n"
 ;
 

src/main.c

@@ -56,7 +56,7 @@ int print_usage(FILE *fp_help){
     fprintf(fp_help,"         eventalign          Align nanopore events to reference k-mers (optimised nanopolish eventalign)\n");
     fprintf(fp_help,"         freq-merge          Merge calculated methylation frequency tsv files\n");
     fprintf(fp_help,"         resquiggle          Align raw signals to basecalled reads\n");
-    fprintf(fp_help,"\nSee the manual page for details (`man ./docs/f5c.1' or https://f5c.page.link/man).\n");
+    fprintf(fp_help,"\nSee the manual page for details (`man ./docs/f5c.1' or https://f5c.bioinf.science/man).\n");
     if(fp_help==stderr){
         exit(EXIT_FAILURE);
     }

src/meth_main.c

@@ -483,7 +483,7 @@ int meth_main(int argc, char* argv[], int8_t mode) {
         fprintf(fp_help,"   -h                         help\n");
         fprintf(fp_help,"   -o FILE                    output to file [stdout]\n");
         fprintf(fp_help,"   -x STR                     parameter profile to be used for better performance (always applied before other options)\n"); //Added option in help
-        fprintf(fp_help,"                              e.g., laptop, desktop, hpc; see https://f5c.page.link/profiles for the full list\n");
+        fprintf(fp_help,"                              e.g., laptop, desktop, hpc; see https://f5c.bioinf.science/profiles for the full list\n");
         fprintf(fp_help,"   --iop INT                  number of I/O processes to read fast5 files [%d]\n",opt.num_iop);
         fprintf(fp_help,"   --pore STR                 set the pore chemistry (r9, r10 or rna004) [r9]\n");
         fprintf(fp_help,"   --slow5 FILE               read from a slow5 file\n");
@@ -536,7 +536,7 @@ int meth_main(int argc, char* argv[], int8_t mode) {
         fprintf(fp_help,"   --profile-cpu=yes|no       process section by section (used for profiling on CPU)\n");
         fprintf(fp_help,"   --write-dump=yes|no        write the fast5 dump to a file or not\n");
         fprintf(fp_help,"   --read-dump=yes|no         read from a fast5 dump file or not\n");
-        fprintf(fp_help,"\nSee the manual page for details (`man ./docs/f5c.1' or https://f5c.page.link/man).\n");
+        fprintf(fp_help,"\nSee the manual page for details (`man ./docs/f5c.1' or https://f5c.bioinf.science/man).\n");
         if(fp_help == stdout){
             exit(EXIT_SUCCESS);
         }

src/resquiggle.c

@@ -42,7 +42,7 @@ static void print_help_msg(FILE *fp_help, opt_t opt){
     fprintf(fp_help,"   -h                         help\n");
     fprintf(fp_help,"   -o FILE                    output to file [stdout]\n");
     fprintf(fp_help,"   -x STR                     parameter profile to be used for better performance (always applied before other options)\n"); //Added option in help
-    fprintf(fp_help,"                              e.g., laptop, desktop, hpc; see https://f5c.page.link/profiles for the full list\n");
+    fprintf(fp_help,"                              e.g., laptop, desktop, hpc; see https://f5c.bioinf.science/profiles for the full list\n");
     fprintf(fp_help,"   -c                         print in paf format\n");
     fprintf(fp_help,"   --verbose INT              verbosity level [%d]\n",opt.verbosity);
     fprintf(fp_help,"   --version                  print version\n");