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change command-line interface to have subcommands (BREAKING)
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@mlin
mlin committed Jul 21, 2018
1 parent 2eb8e4d commit 4bc11fa
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Showing 2 changed files with 78 additions and 39 deletions.
107 changes: 73 additions & 34 deletions src/main.cc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,35 +8,42 @@

using namespace std;

void usage() {
cout << "spvcf: Encode Project VCF to Sparse Project VCF or vice-versa. " << endl;
cout << " " << GIT_REVISION << " " << __TIMESTAMP__ << endl << endl
<< "spvcf [options] [in.vcf|-]" << endl
<< "Reads VCF text from standard input if filename is empty or -" << endl << endl
<< "Options:" << endl
<< " -o,--output out.spvcf Write to out.spvcf instead of standard output" << endl
<< " -d,--decode Decode from the sparse format instead of encoding to" << endl
<< " -p,--period P Ensure checkpoints (full dense rows) at this period or less (default: 1000)" << endl
<< " -q,--quiet Suppress statistics printed to standard error" << endl
<< " -h,--help Show this usage message" << endl << endl
<< "Lossy transformation to increase compression: " << endl
<< " -S,--squeeze Truncate cells to GT:DP, with DP rounded down to a power of two, if: " << endl
<< " - AD is present and indicates zero read depth for alternate alleles; OR" << endl
<< " - VR is present and zero" << endl
<< " Reorders fields within all cells."<< endl << endl;
void help_codec(bool decode) {
if (!decode) {
cout << "spvcf encode: Encode Project VCF to Sparse Project VCF" << endl;
cout << GIT_REVISION << " " << __TIMESTAMP__ << endl << endl
<< "spvcf encode [options] [in.vcf|-]" << endl
<< "Reads VCF text from standard input if filename is empty or -" << endl << endl
<< "Options:" << endl
<< " -o,--output out.spvcf Write to out.spvcf instead of standard output" << endl
<< " -p,--period P Ensure checkpoints (full dense rows) at this period or less (default: 1000)" << endl
<< " -q,--quiet Suppress statistics printed to standard error" << endl
<< " -h,--help Show this help message" << endl << endl
<< "Lossy transformation to increase compression: " << endl
<< " -S,--squeeze Truncate cells to GT:DP, with DP rounded down to a power of two, if: " << endl
<< " - AD is present and indicates zero read depth for alternate alleles; OR" << endl
<< " - VR is present and zero" << endl
<< " Reorders fields within all cells."<< endl << endl;
} else {
cout << "spvcf decode: decode Sparse Project VCF to Project VCF" << endl;
cout << GIT_REVISION << " " << __TIMESTAMP__ << endl << endl
<< "spvcf decode [options] [in.spvcf|-]" << endl
<< "Reads spVCF text from standard input if filename is empty or -" << endl << endl
<< "Options:" << endl
<< " -o,--output out.vcf Write to out.vcf instead of standard output" << endl
<< " -q,--quiet Suppress statistics printed to standard error" << endl
<< " -h,--help Show this help message" << endl << endl;
}
}

int main(int argc, char *argv[]) {
// Parse arguments
int main_codec(int argc, char *argv[], bool decode) {
bool squeeze = false;
bool decode = false;
bool quiet = false;
string output_filename;
uint64_t checkpoint_period = 1000;

static struct option long_options[] = {
{"help", no_argument, 0, 'h'},
{"decode", no_argument, 0, 'd'},
{"squeeze", no_argument, 0, 'S'},
{"period", required_argument, 0, 'p'},
{"quiet", no_argument, 0, 'q'},
Expand All @@ -45,19 +52,24 @@ int main(int argc, char *argv[]) {
};

int c;
while (-1 != (c = getopt_long(argc, argv, "hSdp:qo:",
while (-1 != (c = getopt_long(argc, argv, "hSp:qo:",
long_options, nullptr))) {
switch (c) {
case 'h':
usage();
help_codec(decode);
return 0;
case 'S':
if (decode) {
help_codec(decode);
return -1;
}
squeeze = true;
break;
case 'd':
decode = true;
break;
case 'p':
if (decode) {
help_codec(decode);
return -1;
}
errno=0;
checkpoint_period = strtoull(optarg, nullptr, 10);
if (errno) {
Expand All @@ -71,26 +83,21 @@ int main(int argc, char *argv[]) {
case 'o':
output_filename = string(optarg);
if (output_filename.empty()) {
usage();
help_codec(decode);
return -1;
}
break;
default:
usage();
help_codec(decode);
return -1;
}
}

if (squeeze && decode) {
cerr << "spvcf: --squeeze and --decode should not be specified together" << endl;
return -1;
}

string input_filename;
if (optind == argc-1) {
input_filename = string(argv[optind]);
} else if (optind != argc) {
usage();
help_codec(decode);
return -1;
}

Expand All @@ -105,7 +112,7 @@ int main(int argc, char *argv[]) {
}
input_stream = input_box.get();
} else if (isatty(STDIN_FILENO)) {
usage();
help_codec(decode);
return -1;
}

Expand Down Expand Up @@ -165,3 +172,35 @@ int main(int argc, char *argv[]) {

return 0;
}

void help() {
cout << "spvcf: Sparse Project VCF tool" << endl;
cout << GIT_REVISION << " " << __TIMESTAMP__ << endl << endl
<< "subcommands:" << endl
<< " encode encode Project VCF to spVCF" << endl
<< " decode decode spVCF to Project VCF" << endl
<< " help show this help message" << endl << endl;
}

int main(int argc, char *argv[]) {
if (argc <= 1) {
help();
return -1;
}

string subcommand = argv[1];
if (subcommand == "help" || subcommand == "-h" || subcommand == "--help") {
help();
return 0;
}

optind = 2;
if (subcommand == "encode") {
return main_codec(argc, argv, false);
} else if (subcommand == "decode") {
return main_codec(argc, argv, true);
}

help();
return -1;
}
10 changes: 5 additions & 5 deletions test/spVCF.t
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,15 +13,15 @@ mkdir -p $D
plan tests 13

pigz -dc "$HERE/data/small.vcf.gz" > $D/small.vcf
"$EXE" -o $D/small.spvcf $D/small.vcf
"$EXE" encode -o $D/small.spvcf $D/small.vcf
is "$?" "0" "filename I/O"
is "$(cat $D/small.spvcf | wc -c)" "36942054" "filename I/O output size"

pigz -dc "$HERE/data/small.vcf.gz" | "$EXE" -q > $D/small.spvcf
pigz -dc "$HERE/data/small.vcf.gz" | "$EXE" encode -q > $D/small.spvcf
is "$?" "0" "piped I/O"
is "$(cat $D/small.spvcf | wc -c)" "36942054" "piped I/O output size"

"$EXE" -d -o $D/small.roundtrip.vcf $D/small.spvcf
"$EXE" decode -o $D/small.roundtrip.vcf $D/small.spvcf
is "$?" "0" "decode"
is "$(cat $D/small.roundtrip.vcf | wc -c)" "54007969" "roundtrip decode"

Expand All @@ -33,11 +33,11 @@ is "$(egrep -o "chkptPOS=[0-9]+" $D/small.spvcf | uniq | cut -f2 -d = | tr '\n'
"5030088 5085728 5142746 5225415 5232998 5243839 5252753 5264502 5274001 " \
"checkpoint positions"
"$EXE" -S -p 500 -o $D/small.squeezed.spvcf $D/small.vcf
"$EXE" encode -S -p 500 -o $D/small.squeezed.spvcf $D/small.vcf
is "$?" "0" "squeeze"
is "$(cat $D/small.squeezed.spvcf | wc -c)" "18714203" "squeezed output size"
"$EXE" -d -q -o $D/small.squeezed.roundtrip.vcf $D/small.squeezed.spvcf
"$EXE" decode -q -o $D/small.squeezed.roundtrip.vcf $D/small.squeezed.spvcf
is "$?" "0" "squeezed roundtrip decode"
is "$(cat $D/small.vcf | grep -v ^# | sed -r 's/(\t[^:]+):[^\t]+/\1/g' | sha256sum)" \
"$(cat $D/small.squeezed.roundtrip.vcf | grep -v ^# | sed -r 's/(\t[^:]+):[^\t]+/\1/g' | sha256sum)" \
Expand Down

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