sitepat.c File Reference

#include "binary.h"
#include "boot.h"
#include "rafreader.h"
#include "longvec.h"
#include "misc.h"
#include "strint.h"
#include "error.h"
#include "typedefs.h"
#include <ctype.h>
#include <errno.h>
#include <getopt.h>
#include <gsl/gsl_rng.h>
#include <limits.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>

Data Structures
struct	Stack
	Treat a vector of tipId_t values as a push-down stack. More...

Functions
static void	usage (void)
	Print usage message and die.
static Stack *	Stack_new (int dim, tipId_t buff[dim])
	This stack is local to this file. More...
static void	Stack_free (Stack *stk)
	Frees the stack but not the underlying buffer.
static void	Stack_push (Stack *self, tipId_t x)
	Add an entry to the stack, checking bounds.
static void	generatePatterns (int bit, int npops, Stack *stk, tipId_t pat, int doSing)
	Call as generatePatterns(0, npops, stk, 0); Recursive function, which generates all legal site patterns and pushes them onto a stack.
int	main (int argc, char **argv)

Variables
const char *	useMsg

Function Documentation

Stack_new()

static Stack * Stack_new ( int  dim, tipId_t  buff[dim]  )

static

This stack is local to this file.

It provides a bounds-controlled interface to an external array, which is passed as an argument, buff, to Stack_new.

Variable Documentation

useMsg

const char* useMsg

Initial value:

=
    "\nUsage: sitepat [options] <x>=<in_1> <y>=<in_2> ... outgroup=<in_K>\n"
    "   where <x> and <y> are arbitrary labels, and <in_i> are input\n"
    "   files in raf format. Labels may not include the character \":\".\n"
    "   Final label must be \"outgroup\". Writes to standard output.\n"
    "\n"
    "   If input file name ends with .gz, input is decompressed using\n"
    "   gunzip.\n"