void CommandLineHandlerBase::parse(
const int argc,
const char* argv[],
SuperLogger& logger)
{
ParseResults results;
impl->m_parser.parse(argc, argv, results);
if (impl->m_message_coloring.is_set())
logger.enable_message_coloring();
if (impl->m_message_verbosity.is_set())
set_verbosity(logger, impl->m_message_verbosity.value());
if (impl->m_version.is_set())
print_version_information(logger);
if (impl->m_system.is_set())
print_system_information(logger);
if (impl->m_help.is_set())
{
const string program_name = filesystem::path(argv[0]).filename().string();
print_program_usage(program_name.c_str(), logger);
exit(0);
}
if (impl->m_display_options.is_set())
{
LOG_INFO(logger, "recognized options:");
impl->m_parser.print_recognized_options(logger);
}
results.m_messages.print(logger);
if (results.m_errors > 0 || results.m_warnings > 0)
{
LOG(
logger,
results.m_errors > 0 ? LogMessage::Fatal : LogMessage::Warning,
FMT_SIZE_T " error%s, " FMT_SIZE_T " warning%s encountered while parsing the command line.",
results.m_errors,
results.m_errors > 1 ? "s" : "",
results.m_warnings,
results.m_warnings > 1 ? "s" : "");
}
}
void CommandLineHandlerBase::parse(const int argc, const char* argv[], SuperLogger& logger)
{
impl->m_executable_name = bf::path(argv[0]).filename().string();
impl->m_parser.parse(argc, argv, impl->m_parse_results);
if (impl->m_help.is_set())
{
print_program_usage(impl->m_executable_name.c_str(), logger);
exit(EXIT_SUCCESS);
}
if (impl->m_message_coloring.is_set())
logger.enable_message_coloring();
if (impl->m_message_verbosity.is_set())
logger.set_verbosity_level_from_string(impl->m_message_verbosity.value().c_str());
}
int
main (int argc, char *argv[]) {
char *filename;
char *divstring = NULL, *lasttypestring, *ptr;
Univcoord_T univ_coordstart, univ_coordend;
Chrpos_T coordstart, coordend, lastcoord = 0U;
char Buffer[BUFLEN], nocomment[BUFLEN], query[BUFLEN], typestring[BUFLEN];
int typeint, *types, c;
int nargs, ntypes, ndivs;
int *value_matches = NULL, *matches = NULL;
int n_value_matches = 0, nmatches = 0, i;
int *leftflanks, *rightflanks, nleftflanks = 0, nrightflanks = 0;
long int total;
int n;
IIT_T iit = NULL;
Univ_IIT_T chromosome_iit = NULL;
bool skipp, universalp;
int opt;
extern int optind;
extern char *optarg;
const char *long_name;
int long_option_index = 0;
while ((opt = getopt_long(argc,argv,"a:b:f:LCASUu:c:HRTZN",long_options,&long_option_index)) != -1) {
switch (opt) {
case 0:
long_name = long_options[long_option_index].name;
if (!strcmp(long_name,"version")) {
print_program_version();
exit(0);
} else if (!strcmp(long_name,"help")) {
print_program_usage();
exit(0);
} else if (!strcmp(long_name,"exact")) {
exactp = true;
} else {
/* Shouldn't reach here */
fprintf(stderr,"Don't recognize option %s. For usage, run 'gsnap --help'",long_name);
exit(9);
}
break;
case 'a': lowval = atof(optarg); user_lowvalue_p = true; value_matches_p = true; break;
case 'b': highval = atof(optarg); user_highvalue_p = true; value_matches_p = true; break;
case 'f': fieldstring = optarg; break;
case 'L': force_label_p = true; break;
case 'C': force_coords_p = true; break;
case 'A': annotationonlyp = true; break;
case 'S': sortp = true; break;
case 'U': signedp = false; break;
case 'u': nflanking = atoi(optarg); break;
case 'c': centerp = true; centerlength = atoi(optarg); break;
case 'H': centeruc = true; break;
case 'R': runlengthp = true; break;
case 'T': tallyp = true; break;
case 'Z': zeroesp = true; break;
case 'N': statsp = true; break;
case 'V': print_program_version(); exit(0);
case '?': print_program_usage(); exit(0);
default: exit(9);
}
}
argc -= (optind - 1);
argv += (optind - 1);
if (argc <= 1) {
fprintf(stderr,"Need to specify an iit file. Type \"iit_get --help\" for help.\n");
exit(9);
} else {
filename = argv[1];
}
if (value_matches_p == true) {
if ((iit = IIT_read(filename,/*name*/NULL,true,/*divread*/READ_ALL,/*divstring*/NULL,
/*add_iit_p*/true,/*labels_read_p*/true)) == NULL) {
if (Access_file_exists_p(filename) == false) {
fprintf(stderr,"Cannot read file %s\n",filename);
} else {
fprintf(stderr,"File %s appears to be an invalid IIT file\n",filename);
}
exit(9);
} else if (fieldstring != NULL) {
if ((fieldint = IIT_fieldint(iit,fieldstring)) < 0) {
fprintf(stderr,"No field %s defined in iit file.\n",fieldstring);
exit(9);
}
}
if (IIT_valuep(iit) == false) {
fprintf(stderr,"Error: This IIT file does not have values stored\n");
exit(9);
}
if (user_lowvalue_p == true && user_highvalue_p == true) {
if (lowval > highval) {
fprintf(stderr,"Cannot have lowval %f > highval %f\n",lowval,highval);
exit(9);
} else {
value_matches = IIT_get_values_between(&n_value_matches,iit,lowval,highval,/*sortp*/false);
}
} else if (user_lowvalue_p == true) {
value_matches = IIT_get_values_above(&n_value_matches,iit,lowval,/*sortp*/false);
} else { /* user_highvalue_p == true */
value_matches = IIT_get_values_below(&n_value_matches,iit,highval,/*sortp*/false);
}
}
if (0 && statsp == true && argc == 2) {
/* Want total over entire IIT */
if ((iit = IIT_read(filename,NULL,true,/*divread*/READ_ALL,/*divstring*/NULL,/*add_iit_p*/true,
/*labels_read_p*/false)) == NULL) {
if (Access_file_exists_p(filename) == false) {
fprintf(stderr,"Cannot read file %s\n",filename);
} else {
fprintf(stderr,"File %s appears to be an invalid IIT file\n",filename);
}
exit(9);
} else if (fieldstring != NULL) {
if ((fieldint = IIT_fieldint(iit,fieldstring)) < 0) {
fprintf(stderr,"No field %s defined in iit file.\n",fieldstring);
exit(9);
}
}
total = 0;
n = 0;
for (i = 0; i < IIT_total_nintervals(iit); i++) {
debug(printf("index = %d\n",matches[i]));
compute_totals_tally(&total,&n,/*coordstart*/0,/*coordend*/-1U,i,iit);
}
printf("counts:%ld non-zero-positions:%u mean-over-nonzero:%.3f\n",total,n,(double) total/(double) n);
IIT_free(&iit);
return 0;
} else if ((universalp = IIT_universalp(filename,/*add_iit_p*/true)) == true) {
chromosome_iit = Univ_IIT_read(filename,/*readonlyp*/true,/*add_iit_p*/true);
if (argc != 3) {
fprintf(stderr,"For chromosome IIT file, need to specify a query on the command line\n");
exit(9);
} else {
/* Try as 0:<iitfile> 1:<query> */
matches = get_matches_univ(&nmatches,&divstring,&univ_coordstart,&univ_coordend,
&leftflanks,&nleftflanks,&rightflanks,&nrightflanks,
argv[2],/*typestring*/NULL,&chromosome_iit,filename);
for (i = 0; i < nmatches; i++) {
debug(printf("\nindex = %d\n",matches[i]));
print_interval_univ(univ_coordstart,univ_coordend,matches[i],chromosome_iit);
}
}
if (divstring != NULL) {
FREE(divstring);
}
Univ_IIT_free(&chromosome_iit);
return 0;
} else if (argc == 2 && value_matches_p == true) {
/* Note: Could potentially handle input from stdin, but currently just deal with value_matches */
ndivs = IIT_ndivs(iit);
for (i = 0; i < n_value_matches; i++) {
debug(printf("\nindex = %d\n",matches[i]));
print_interval(&lastcoord,/*total*/0,/*divstring*/NULL,/*coordstart*/0,/*coordend*/0,
value_matches[i],iit,ndivs,fieldint);
}
FREE(value_matches);
IIT_free(&iit);
return 0;
} else if (argc == 2) {
debug(printf("Running under argc 2\n"));
/* Expecting input from stdin */
if ((iit = IIT_read(filename,NULL,true,/*divread*/READ_ALL,/*divstring*/NULL,/*add_iit_p*/true,
/*labels_read_p*/true)) == NULL) {
if (Access_file_exists_p(filename) == false) {
fprintf(stderr,"Cannot read file %s\n",filename);
} else {
fprintf(stderr,"File %s appears to be an invalid IIT file\n",filename);
}
exit(9);
} else if (fieldstring != NULL) {
if ((fieldint = IIT_fieldint(iit,fieldstring)) < 0) {
fprintf(stderr,"No field %s defined in iit file.\n",fieldstring);
exit(9);
}
}
while (fgets(Buffer,BUFLEN,stdin) != NULL) {
if ((ptr = rindex(Buffer,'\n')) != NULL) {
*ptr = '\0';
}
strcpy(nocomment,Buffer);
if ((ptr = rindex(nocomment,'#')) != NULL) {
*ptr = '\0';
}
skipp = false;
if ((nargs = sscanf(nocomment,"%s %s",query,typestring)) == 2) {
debug(printf("typestring is %s\n",typestring));
matches = get_matches(&nmatches,&divstring,&univ_coordstart,&univ_coordend,
&leftflanks,&nleftflanks,&rightflanks,&nrightflanks,
query,typestring,&iit,filename);
coordstart = (Chrpos_T) univ_coordstart;
coordend = (Chrpos_T) univ_coordend;
} else if (nargs == 1) {
debug(printf("typestring is NULL\n"));
matches = get_matches(&nmatches,&divstring,&univ_coordstart,&univ_coordend,
&leftflanks,&nleftflanks,&rightflanks,&nrightflanks,
query,/*typestring*/NULL,&iit,filename);
coordstart = (Chrpos_T) univ_coordstart;
coordend = (Chrpos_T) univ_coordend;
} else {
fprintf(stderr,"Can't parse line %s. Ignoring.\n",nocomment);
skipp = true;
}
total = 0;
if (skipp == false) {
fprintf(stdout,"# Query: %s\n",Buffer);
ndivs = IIT_ndivs(iit);
if (nflanking > 0) {
for (i = nleftflanks-1; i >= 0; i--) {
debug(printf("\nleft index = %d\n",leftflanks[i]));
print_interval(&lastcoord,/*total*/0,divstring,coordstart,coordend,leftflanks[i],iit,ndivs,fieldint);
}
printf("====================\n");
FREE(leftflanks);
}
lastcoord = coordstart;
for (i = 0; i < nmatches; i++) {
debug(printf("\nindex = %d\n",matches[i]));
total = print_interval(&lastcoord,total,divstring,coordstart,coordend,matches[i],iit,ndivs,fieldint);
}
if (nflanking > 0) {
printf("====================\n");
for (i = 0; i < nrightflanks; i++) {
debug(printf("\nright index = %d\n",rightflanks[i]));
print_interval(&lastcoord,/*total*/0,divstring,coordstart,coordend,rightflanks[i],iit,ndivs,fieldint);
}
FREE(rightflanks);
}
if (zeroesp == true) {
while (lastcoord <= coordend) {
printf("%s\t%u\t%d\n",divstring,lastcoord,0);
lastcoord++;
}
}
}
if (divstring != NULL) {
FREE(divstring);
}
FREE(matches);
printf("%ld\n",total);
fprintf(stdout,"# End\n");
fflush(stdout);
}
IIT_free(&iit);
return 0;
} else {
/* Get coordinates/type from command line */
if (argc == 3) {
/* Try as 0:<iitfile> 1:<query> */
matches = get_matches(&nmatches,&divstring,&univ_coordstart,&univ_coordend,
&leftflanks,&nleftflanks,&rightflanks,&nrightflanks,
argv[2],/*typestring*/NULL,&iit,filename);
coordstart = (Chrpos_T) univ_coordstart;
coordend = (Chrpos_T) univ_coordend;
} else if (argc == 4) {
/* Try as 0:<iitfile> 1:<query> 2:<type> */
debug(printf("Running under argc 4\n"));
matches = get_matches(&nmatches,&divstring,&univ_coordstart,&univ_coordend,
&leftflanks,&nleftflanks,&rightflanks,&nrightflanks,
argv[2],argv[3],&iit,filename);
coordstart = (Chrpos_T) univ_coordstart;
coordend = (Chrpos_T) univ_coordend;
} else {
types = (int *) CALLOC(argc-3,sizeof(int));
for (c = 3, ntypes = 0; c < argc; c++) {
if ((typeint = IIT_typeint(iit,argv[c])) < 0) {
fprintf(stderr,"No such type as %s. Ignoring the type.\n",argv[c]);
} else {
types[ntypes++] = typeint;
lasttypestring = argv[c];
}
}
if (ntypes == 0) {
matches = get_matches(&nmatches,&divstring,&univ_coordstart,&univ_coordend,
&leftflanks,&nleftflanks,&rightflanks,&nrightflanks,
argv[2],/*typestring*/NULL,&iit,filename);
coordstart = (Chrpos_T) univ_coordstart;
coordend = (Chrpos_T) univ_coordend;
} else if (ntypes == 1) {
matches = get_matches(&nmatches,&divstring,&univ_coordstart,&univ_coordend,
&leftflanks,&nleftflanks,&rightflanks,&nrightflanks,
argv[2],lasttypestring,&iit,filename);
coordstart = (Chrpos_T) univ_coordstart;
coordend = (Chrpos_T) univ_coordend;
} else {
matches = get_matches_multiple_typed(&nmatches,&divstring,&univ_coordstart,&univ_coordend,
&leftflanks,&nleftflanks,&rightflanks,&nrightflanks,
argv[2],types,ntypes,&iit,filename);
coordstart = (Chrpos_T) univ_coordstart;
coordend = (Chrpos_T) univ_coordend;
}
}
if (value_matches_p == true) {
matches = match_intersection(&nmatches,/*matches1*/matches,/*nmatches1*/nmatches,
/*matches2*/value_matches,/*nmatches2*/n_value_matches);
FREE(value_matches);
}
#if 0
if (centerp == true) {
print_spaces(centerlength);
printf("*");
print_spaces(centerlength-1);
printf("\n");
}
#endif
if (statsp == true) {
total = 0;
n = 0;
for (i = 0; i < nmatches; i++) {
debug(printf("index = %d\n",matches[i]));
compute_totals_tally(&total,&n,coordstart,coordend,matches[i],iit);
}
n = coordend - coordstart + 1;
printf("counts:%ld width:%u mean:%.3f\n",total,n,(double)total/(double) n);
#if 0
} else if (geomeanp == true) {
logtotal = 0.0;
total = 0;
n = 0;
for (i = 0; i < nmatches; i++) {
debug(printf("index = %d\n",matches[i]));
logtotal = compute_logtotal_tally(&total,&n,coordstart,coordend,matches[i],iit);
}
printf("geomean:%f totalcounts:%ld posrange:%d\n",
exp(logtotal/(double) (coordend - coordstart + 1)) - 1.0,total,n);
#endif
} else {
ndivs = IIT_ndivs(iit);
if (nflanking > 0) {
for (i = nleftflanks-1; i >= 0; i--) {
debug(printf("\nleft index = %d\n",leftflanks[i]));
print_interval(&lastcoord,/*total*/0,divstring,coordstart,coordend,leftflanks[i],iit,ndivs,fieldint);
}
printf("====================\n");
FREE(leftflanks);
}
lastcoord = coordstart;
for (i = 0; i < nmatches; i++) {
debug(printf("\nindex = %d\n",matches[i]));
print_interval(&lastcoord,/*total*/0,divstring,coordstart,coordend,matches[i],iit,ndivs,fieldint);
}
if (nflanking > 0) {
printf("====================\n");
for (i = 0; i < nrightflanks; i++) {
debug(printf("\nright index = %d\n",rightflanks[i]));
print_interval(&lastcoord,/*total*/0,divstring,coordstart,coordend,rightflanks[i],iit,ndivs,fieldint);
}
FREE(rightflanks);
}
}
if (divstring != NULL) {
FREE(divstring);
}
FREE(matches);
IIT_free(&iit);
return 0;
}
}
