mapmix.c File Reference

#include "branchtab.h"
#include "error.h"
#include "lblndx.h"
#include "misc.h"
#include "rafreader.h"
#include "strdblqueue.h"
#include "typedefs.h"
#include <ctype.h>
#include <errno.h>
#include <getopt.h>
#include <limits.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
#include <unistd.h>

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

Macros
#define	BUFFSIZE   1024

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.
static FILE *	openOutput (const char *chr)
	Open a file named <chr>.mapmix for output, or abort if that file already exists or cannot be opened for writing. More...
int	main (int argc, char **argv)

Variables
const char *	useMsg

Function Documentation

openOutput()

static FILE * openOutput ( const char *  chr )

static

Open a file named <chr>.mapmix for output, or abort if that file already exists or cannot be opened for writing.

Return pointer to opened file.

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: mapmix --admix <fraction> --zero <a.legosim>"
    " --one <b.legosim>\\\n"
    "   <x>=<in_1> <y>=<in_2> ... outgroup=<in_K>\n\n"
    "   where <fraction> is the admixture fraction as estimated by legofit,\n"
    "   <a.legosim> is a file containing the results of a legosim run\n"
    "   with parameters as fitted by legofit, except that one admixture\n"
    "   fraction is set to 0, <b.legosim> is like <a.legosim> except\n"
    "   that this admixture fraction is set to 1, <x> and <y> are arbitrary\n"
    "   labels, and <in_i> are input files in raf format. Labels may not\n"
    "   include the character \":\". Final label must be \"outgroup\".\n"
    "   Writes to a series of files with names like 1.mapmix, X.mapmix,\n"
    "   etc, where \"1\" and \"X\" are the names of chromosomes. If these\n"
    "   files already exist, the program aborts.\n"
    "\n"
    "   If <in_i> file name ends with .gz, input is decompressed using\n"
    "   gunzip.\n"