Description: Fix exit codes to be successful and output to stdout. Author: Lance Lin Last-Update: 2024-01-19 --- stacks.orig/scripts/stacks-gdb +++ stacks/scripts/stacks-gdb @@ -28,10 +28,10 @@ " if [[ $# -eq 0 ]] ;then - echo -n "$usage" >&2 + echo -n "$usage" echo echo -n "$gdb_req" - exit 1 + exit 0 fi if ! command -v gdb &>/dev/null ;then --- stacks.orig/scripts/stacks-samtools-tview +++ stacks/scripts/stacks-samtools-tview @@ -28,15 +28,15 @@ sample= if (( $# == 0 )) ;then echo -n "$help" - exit 1 + exit 0 fi while getopts 'vhP:c:s:' op ;do case $op in P) dir="$OPTARG" ;; c) locus="$OPTARG" ;; s) sample="$OPTARG" ;; - h) echo -n "$help"; exit 1 ;; - v) echo "$stacks_version"; exit 1 ;; + h) echo -n "$help"; exit 0 ;; + v) echo "$stacks_version"; exit 0 ;; *) echo "ERROR: while parsing arguments." >&2; exit 1 ;; esac done --- stacks.orig/src/sstacks.cc +++ stacks/src/sstacks.cc @@ -1429,13 +1429,13 @@ } void version() { - cerr << "sstacks " << VERSION << "\n\n"; + cout << "sstacks " << VERSION << "\n\n"; - exit(1); + exit(0); } void help() { - cerr << "sstacks " << VERSION << "\n" + cout << "sstacks " << VERSION << "\n" << "sstacks -P dir -M popmap [-t n_threads]" << "\n" << "sstacks -c catalog_path -s sample_path [-s sample_path ...] -o path [-t n_threads]" << "\n" << " -P,--in-path: path to the directory containing Stacks files.\n" @@ -1451,10 +1451,10 @@ ; #ifdef DEBUG - cerr << "\n" + cout << "\n" "Debug options:\n" " --write-all-matches: Write blacklisted matches. (Compatibility with the web interface?)\n"; #endif - exit(1); + exit(0); } --- stacks.orig/src/process_radtags.cc +++ stacks/src/process_radtags.cc @@ -2566,13 +2566,13 @@ } void version() { - cerr << "process_radtags " << VERSION << "\n\n"; + cout << "process_radtags " << VERSION << "\n\n"; - exit(1); + exit(0); } void help() { - cerr << "process_radtags " << VERSION << "\n" + cout << "process_radtags " << VERSION << "\n" << "process_radtags -p in_dir [-P] [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len]\n" << "process_radtags -f in_file [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len]\n" << "process_radtags --in-path in_dir [--paired] [--barcodes barcode_file] --out-path out_dir --renz-1 enz [--renz-2 enz] [--threads num] [-c] [-q] [-r] [-t len]\n" @@ -2613,20 +2613,20 @@ uint cnt = renz_cnt.size(); it = renz_cnt.begin(); for (uint i = 1; i <= cnt; i++) { - cerr << "'" << it->first << "'"; + cout << "'" << it->first << "'"; if (i < cnt - 1) - cerr << ", "; + cout << ", "; else if (i == cnt - 1) - cerr << ", or "; + cout << ", or "; if (i % 8 == 0) - cerr << "\n "; + cout << "\n "; it++; } - cerr << "\n"; + cout << "\n"; - cerr << "\n" + cout << "\n" << " Protocol-specific options:\n" << " --bestrad: library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads.\n" << " --methylrad: library was generated using enzymatic methyl-seq (EM-seq) or bisulphite sequencing.\n\n" @@ -2651,5 +2651,5 @@ << " --barcode-dist-1: the number of allowed mismatches when rescuing single-end barcodes (default 1).\n" << " --barcode-dist-2: the number of allowed mismatches when rescuing paired-end barcodes (defaults to --barcode-dist-1).\n"; - exit(1); + exit(0); } --- stacks.orig/scripts/denovo_map.pl +++ stacks/scripts/denovo_map.pl @@ -920,13 +920,13 @@ } sub version { - print STDERR "denovo_map.pl ", stacks_version, "\n"; + print STDOUT "denovo_map.pl ", stacks_version, "\n"; } sub usage { version(); - print STDERR <: specify k-mer size for matching between between catalog loci (automatically calculated by default).\n" << " --report-mmatches: report query loci that match more than one catalog locus.\n"; - exit(1); + exit(0); } --- stacks.orig/src/phasedstacks.cc +++ stacks/src/phasedstacks.cc @@ -1938,13 +1938,13 @@ } void version() { - cerr << "phasedstacks " << VERSION << "\n\n"; + cout << "phasedstacks " << VERSION << "\n\n"; - exit(1); + exit(0); } void help() { - cerr << "phasedstacks " << VERSION << "\n" + cout << "phasedstacks " << VERSION << "\n" << "phasedstacks -b id -S path -P path -t file_type [-p threads] [-M popmap] [-v] [-h]" << "\n" << " b: Stacks batch ID.\n" << " P: path to the phased output files.\n" @@ -1963,5 +1963,5 @@ << " --min-inform-pairs: when building D' haplotype blocks, the minimum number of informative D' measures to combine two blocks (default 0.9).\n\n"; - exit(1); + exit(0); } --- stacks.orig/src/populations.cc +++ stacks/src/populations.cc @@ -4384,5 +4384,5 @@ #endif ; - exit(1); + exit(0); } --- stacks.orig/src/process_shortreads.cc +++ stacks/src/process_shortreads.cc @@ -1120,13 +1120,13 @@ } void version() { - cerr << "process_shortreads " << VERSION << "\n\n"; + cout << "process_shortreads " << VERSION << "\n\n"; - exit(1); + exit(0); } void help() { - cerr << "process_shortreads " << VERSION << "\n" + cout << "process_shortreads " << VERSION << "\n" << "process_shortreads [-f in_file | -p in_dir [-P] [-I] | -1 pair_1 -2 pair_2] -b barcode_file -o out_dir [-i type] [-y type] [-c] [-q] [-r] [-E encoding] [-t len] [-D] [-w size] [-s lim] [-h]\n" << " f: path to the input file if processing single-end seqeunces.\n" << " i: input file type, either 'bustard' for the Illumina BUSTARD format, 'bam', 'fastq' (default), or 'gzfastq' for gzipped FASTQ.\n" @@ -1170,5 +1170,5 @@ << " --mate-pair: raw reads are circularized mate-pair data, first read will be reverse complemented.\n" << " --no-overhang: data does not contain an overhang nucleotide between barcode and seqeunce.\n"; - exit(1); + exit(0); } --- stacks.orig/src/ustacks.cc +++ stacks/src/ustacks.cc @@ -3013,13 +3013,13 @@ } void version() { - cerr << "ustacks " << VERSION << "\n\n"; + cout << "ustacks " << VERSION << "\n\n"; - exit(1); + exit(0); } void help() { - cerr << "ustacks " << VERSION << "\n" + cout << "ustacks " << VERSION << "\n" << "ustacks -f in_path -o out_path [-M max_dist] [-m min_reads] [-t num_threads]" << "\n" << " -f,--file: input file path.\n" << " -o,--out-path: output path to write results.\n" @@ -3055,5 +3055,5 @@ << "\n" << " h: display this help message.\n"; - exit(1); + exit(0); } --- stacks.orig/src/kmer_filter.cc +++ stacks/src/kmer_filter.cc @@ -1800,13 +1800,13 @@ } void version() { - cerr << "kmer_filter " << VERSION << "\n\n"; + cout << "kmer_filter " << VERSION << "\n\n"; - exit(1); + exit(0); } void help() { - cerr << "kmer_filter " << VERSION << "\n" + cout << "kmer_filter " << VERSION << "\n" << "kmer_filter [-f in_file_1 [-f in_file_2...] | -p in_dir] [-1 pair_1 -2 pair_2 [-1 pair_1...]] -o out_dir [-i type] [-y type] [-D] [-h]\n" << " f: path to the input file if processing single-end seqeunces.\n" << " i: input file type, either 'bustard' for the Illumina BUSTARD output files, 'fasta', 'fastq', 'gzfasta', or 'gzfastq' (default 'fastq').\n" @@ -1834,5 +1834,5 @@ << " --read-k-freq : read a set of kmers along with their frequencies of occurrence instead of reading raw input files.\n" << "\n"; - exit(1); + exit(0); }