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#include "pilercr.h"
struct VALUE_OPT
{
const char *m_pstrName;
const char *m_pstrValue;
};
struct FLAG_OPT
{
const char *m_pstrName;
bool m_bSet;
};
static VALUE_OPT ValueOpts[] =
{
"in", 0,
"minhitlength", 0,
"minid", 0,
"maxmem", 0,
"log", 0,
"loga", 0,
"out", 0,
"hits", 0,
"discardedhits", 0,
"piles", 0,
"filterout", 0,
"diameter", 0,
"traps", 0,
"fhits", 0,
"seq", 0,
"cmp", 0,
"ref", 0,
"minrepeat", 0,
"maxrepeat", 0,
"minspacer", 0,
"maxspacer", 0,
"minrepeatratio", 0,
"minspacerratio", 0,
"minarray", 0,
"mincons", 0,
};
static int ValueOptCount = sizeof(ValueOpts)/sizeof(ValueOpts[0]);
static FLAG_OPT FlagOpts[] =
{
"quiet", 0,
"version", 0,
"help", 0,
"options", 0,
"loghits", 0,
"logtraps", 0,
"showhits", 0,
"loghits", 0,
"logimages", 0,
"logalns", 0,
"noinfo", 0,
"segv", 0,
"trimseqs", 0,
};
static int FlagOptCount = sizeof(FlagOpts)/sizeof(FlagOpts[0]);
void CommandLineError(const char *Format, ...)
{
va_list ArgList;
va_start(ArgList, Format);
char Str[4096];
vsprintf(Str, Format, ArgList);
Usage();
fprintf(stderr, "\n*** Invalid command line ***\n");
fprintf(stderr, "%s\n", Str);
exit(1);
}
static bool TestSetFlagOpt(const char *Arg)
{
for (int i = 0; i < FlagOptCount; ++i)
if (!stricmp(Arg, FlagOpts[i].m_pstrName))
{
FlagOpts[i].m_bSet = true;
return true;
}
return false;
}
static bool TestSetValueOpt(const char *Arg, const char *Value)
{
for (int i = 0; i < ValueOptCount; ++i)
if (!stricmp(Arg, ValueOpts[i].m_pstrName))
{
if (0 == Value)
CommandLineError("Option -%s must have value\n", Arg);
ValueOpts[i].m_pstrValue = strsave(Value);
return true;
}
return false;
}
bool FlagOpt(const char *Name)
{
for (int i = 0; i < FlagOptCount; ++i)
if (!stricmp(Name, FlagOpts[i].m_pstrName))
return FlagOpts[i].m_bSet;
Quit("FlagOpt(%s) invalid", Name);
return false;
}
const char *ValueOpt(const char *Name)
{
for (int i = 0; i < ValueOptCount; ++i)
if (!stricmp(Name, ValueOpts[i].m_pstrName))
return ValueOpts[i].m_pstrValue;
Quit("ValueOpt(%s) invalid", Name);
return 0;
}
const char *RequiredValueOpt(const char *Name)
{
const char *s = ValueOpt(Name);
if (0 == s)
CommandLineError("Required option -%s not specified\n", Name);
return s;
}
void ProcessArgVect(int argc, char *argv[])
{
if (argc == 0)
{
Usage();
exit(0);
}
if (argc == 1)
{
if (strcmp("-help", argv[0]) == 0 || strcmp("--help", argv[0]) == 0)
{
Usage();
exit(0);
}
}
for (int iArgIndex = 0; iArgIndex < argc; )
{
const char *Arg = argv[iArgIndex];
if (Arg[0] != '-')
Quit("Command-line option \"%s\" must start with '-'\n", Arg);
const char *ArgName = Arg + 1;
if (TestSetFlagOpt(ArgName))
{
++iArgIndex;
continue;
}
char *Value = 0;
if (iArgIndex < argc - 1)
Value = argv[iArgIndex+1];
if (TestSetValueOpt(ArgName, Value))
{
iArgIndex += 2;
continue;
}
CommandLineError("Invalid command line option \"%s\"\n", ArgName);
}
}
void IntOpt(const char *Name, int *ptrValue)
{
const char *strValue = ValueOpt(Name);
if (strValue != 0)
*ptrValue = atoi(strValue);
}
void FloatOpt(const char *Name, double *ptrValue)
{
const char *strValue = ValueOpt(Name);
if (strValue != 0)
*ptrValue = atof(strValue);
}
void Options()
{
fprintf(stderr,
"\n"
"\n"
"Basic options:\n"
" -in <filename> Sequence file to analyze (FASTA format).\n"
" -out <filename> Report file name (plain text).\n"
" -seq <filename> Save consensus sequences to this FASTA file.\n"
" -trimseqs Eliminate similar seqs from -seq file.\n"
" -noinfo Don't write help to report file.\n"
" -quiet Don't write progress messages to stderr.\n"
"\n"
"Criteria for CRISPR detection, defaults in parentheses:\n"
" -minarray <N> Must be at least <n> repeats in array (3).\n"
" -mincons <F> Minimum conservation (0.9).\n"
" At least N repeats must have identity\n"
" >= F with the consensus sequence.\n"
" Value is in range 0 .. 1.0.\n"
" It is recommended to use a value < 1.0\n"
" because using 1.0 may suppress true\n"
" arrays due to boundary misidentification.\n"
" -minrepeat <L> Minimum repeat length (16).\n"
" -maxrepeat <L> Maximum repeat length (64).\n"
" -minspacer <L> Minimum spacer length (8).\n"
" -maxspacer <L> Maximum spacer length (64).\n"
" -minrepeatratio <R> Minimum repeat ratio (0.9).\n"
" -minspacerratio <R> Minimum spacer ratio (0.75).\n"
" 'Ratios' are defined as minlength / maxlength,\n"
" thus a value close to 1.0 requires lengths to\n"
" be similar, 1.0 means identical lengths.\n"
" Spacer lengths sometimes vary significantly, so\n"
" the default ratio is smaller. As with -mincons,\n"
" using 1.0 is not recommended.\n"
"\n"
"Parameters for creating local alignments:\n"
" -minhitlength <L> Minimum alignment length (16).\n"
" -minid <F> Minimum identity (0.94).\n"
"\n"
"\n"
);
}
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