08-09-2012
If there are N rows in genotype.bim, there are 2N+2 columns in each row of genotype.ped?
Also, how large are these files? If they are humongous, it would help to know in advance, lest time is wasted on an unsuitable approach. If the files are very large, it would help to know something about the hardware (available ram, free storage, etc).
Regards,
Alister
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LEARN ABOUT OPENDARWIN
funtablerowget
funtablerowget(3) SAORD Documentation funtablerowget(3)
NAME
FunTableRowGet - get Funtools rows
SYNOPSIS
#include <funtools.h>
void *FunTableRowGet(Fun fun, void *rows, int maxrow, char *plist,
int *nrow)
DESCRIPTION
The FunTableRowGet() routine retrieves rows from a Funtools binary table or raw event file, and places the values of columns selected by
FunColumnSelect() into an array of user structs. Selected column values are automatically converted to the specified user data type (and
to native data format) as necessary.
The first argument is the Fun handle associated with this row data. The second rows argument is the array of user structs into which the
selected columns will be stored. If NULL is passed, the routine will automatically allocate space for this array. (This includes proper
allocation of pointers within each struct, if the "@" pointer type is used in the selection of columns. Note that if you pass NULL in the
second argument, you should free this space using the standard free() system call when you are finished with the array of rows.) The third
maxrow argument specifies the maximum number of rows to be returned. Thus, if rows is allocated by the user, it should be at least of size
maxrow*sizeof(evstruct).
The fourth plist argument is a param list string. Currently, the keyword/value pair "mask=transparent" is supported in the plist argument.
If this string is passed in the call's plist argument, then all rows are passed back to the user (instead of just rows passing the filter).
This is only useful when FunColumnSelect() also is used to specify "$region" as a column to return for each row. In such a case, rows
found within a region have a returned region value greater than 0 (corresponding to the region id of the region in which they are located),
rows passing the filter but not in a region have region value of -1, and rows not passing any filter have region value of 0. Thus, using
"mask=transparent" and the returned region value, a program can process all rows and decide on an action based on whether a given row
passed the filter or not.
The final argument is a pointer to an int variable that will return the actual number of rows returned. The routine returns a pointer to
the array of stored rows, or NULL if there was an error. (This pointer will be the same as the second argument, if the latter is
non-NULL).
/* get rows -- let routine allocate the row array */
while( (buf = (Ev)FunTableRowGet(fun, NULL, MAXROW, NULL, &got)) ){
/* process all rows */
for(i=0; i<got; i++){
/* point to the i'th row */
ev = buf+i;
/* rearrange some values. etc. */
ev->energy = (ev->pi+ev->pha)/2.0;
ev->pha = -ev->pha;
ev->pi = -ev->pi;
}
/* write out this batch of rows */
FunTableRowPut(fun2, buf, got, 0, NULL);
/* free row data */
if( buf ) free(buf);
}
As shown above, successive calls to FunTableRowGet() will return the next set of rows from the input file until all rows have been read,
i.e., the routine behaves like sequential Unix I/O calls such as fread(). See evmerge example code for a more complete example.
Note that FunTableRowGet() also can be called as FunEventsGet(), for backward compatibility.
SEE ALSO
See funtools(7) for a list of Funtools help pages
version 1.4.2 January 2, 2008 funtablerowget(3)