VGPirpbin

Text to binary and binary to text converter for the IRP file format

usage

Convert IRP text to binary

VGPirpbin a2b reads.bsq reads.irp

This conversion performs multiple scans of the file reads.irp to compute statistics for redundancy coding, so reads.irp needs to be a regular file. The maximum number of lines scanned for obtaining statistics can be set using the maxstatlines swich (i.e. set e.g. --maxstatlines50000).

Convert binary IRP to text

VGPirpbin b2a reads.bsq > reads.irp

The binary to text conversion supports ranges via the --from and --to switches, e.g.:

VGPirpbin b2a --from50 --to100 reads.bsq > reads.irp

Note that not converting the whole binary file to text form will produce a file without a header.

building

The VGPirpbin comes with a Makefile which will build the VGPirpbin and an accompanying library for accessing binary IRP files from C programs. For building those just run make. The C compiler used can be set via the CC variable, e.g.

CC=gcc make

installation

The package can be installed via

make install

The default installation path is /usr/local. This can be changed using the PREFIX variable when calling make install:

PREFIX=${HOME}/vgp make install

using the library in C code

Here is a short example for accessing binary IRP files from C code. The code reads a binary IRP file and outputs the records in FastA format.

#include "VGPirpbin_decodeBinaryFile.h"
#include <stdio.h>
#include <stdlib.h>

int main(int argc, char * argv[])
{
	int returncode = EXIT_SUCCESS;
        IRPBINDecoder * I = NULL;
        IRPBinDecoderContext * context = NULL;
        char const * fn = NULL;
        int done = 0;
        unsigned long id = 0;

	if ( argc < 2 )
	{
		fprintf(stderr,"usage: %s <in>\n", argv[0]);
		return EXIT_FAILURE;
	}
	
	fn = argv[1];

	/* open file */
	if ( ! (I = IRPBINDecoder_allocateFromFile(fn)) )
	{
		fprintf(stderr,"Unable to open file\n");
		returncode = EXIT_FAILURE;
                goto cleanup;
        }

	/* get decoder context */
        if (!(context = IRPBINDecoder_getContext(I)))
        {
                returncode = -1;
                goto cleanup;
        }
        
        /* print number of pairs in file */
        fprintf(stderr,"found %lu pairs in file\n", I->nr);
        
        while ( ! done )
        {
		int const r0 = IRPBINDecoder_decodePair(I,context);
        
		/* decode error */
		if ( r0 < 0 )
		{
			fprintf(stderr,"Decoding failed\n");
			returncode = EXIT_FAILURE;
			goto cleanup;
		}
		/* end of file */
		else if ( r0 == 0 )
		{
			done = 1;
		}
		/* pair */
		else if ( r0 == 1 )
		{
			/* first mate (0 terminated) */
			char const * seq_a = context->DF->S;
			/* length of forward sequence */
			/* uint64_t seq_a_len = context->DF->S_l; */
			fprintf(stdout,">%lu/1\n",id);
			fprintf(stdout,"%s\n",seq_a);

			/* second mate (0 terminated) */
			char const * seq_b = context->DR->S;
			/* length of forward sequence */
			/* uint64_t seq_b_len = context->DR->S_l; */
			fprintf(stdout,">%lu/2\n",id);
			fprintf(stdout,"%s\n",seq_b);
			
			id += 1;
		}
        }

	cleanup:
	IRPBinDecoderContext_deallocate(context);
	IRPBINDecoder_deallocate(I);

	return returncode;
}

Assuming the code is saved as IRPtoFastA.c, the program can be compiled using

cc -I${HOME}/vgp/include IRPtoFastA.c -o IRPtoFastA -L${HOME}/vgp/lib -lVGPirpbin

if VGPirpbin has previously been installed at ${HOME}/vgp (using PREFIX=$HOME/vgp make install).

The function IRPBINDecoder_seek can be used to position the input pointer at a given pair id in the input file:

/* seek to pair number 5 in the file */
IRPBINDecoder_seek(I,context,5);

The return value of the function should be checked. It returns 0 for success and -1 otherwise.

Note that while the IRPBINDecoder data structure can be shared across threads, this is not true for IRPBinDecoderContext. You need to create a separate context for each thread (concurrently) accessing an input file.