znt:

======================================================================================================= The Zero-Initialized Template (znt) is a container format for each chromosome and a wrapper capable to combine multiple streams of data from disparate sources into a coherent record. (machine readable wrapper format for genome annotation and information exchange protocol standard. These files provided a good template for writing sequence reads, for example.

Algorithm

The first step is to create a large array file per chromosome and initialize to zero.

Step 1: count the number of nucleotides (n) in each chromosome Step 2: For (n = 0; n < chrLen; n++) {

                fwrite(&nVal                    /* file pointer pointing to address in memory */ 
                sizeof(X)-see below ,1,fp);     /* reserve a chunk of memory with size (X) initialize to zero */
               
          }

** where: X= char, short int, long int

Format Specifications Summary Table: Name Type Size Range

znt char 1 (8-bit) byte 0 to 255 | /*char type */
znt2 int 2 (16-bit) byte 0 to 65,535 | /*short int */
znt4 long int 4 (32-bit) bytes 0 to 4,294,967,295 | /*full int */

Utilities:

• Program name: * Description:

init_hsG37.................program to initialize binary hs chromosome files to zeros that is designed to fwrite/fread binary 1 byte files init_hg19..................program to initialize binary hs chromosome files to zeros that is designed to fread/fwrite binary 2 byte files init_hsG32.................program to initialize binary chromosome files to zeros that is designed to fread/fwrite binary 4 byte files