sparse-CRAM 0.1.6.3

A Basic Reader and Writer for CRAM format

Compressed Row-Access Matrix file format.

Goal : Simple and Efficient storage of 2d sparse matrices for memory efficient access of rows columns and ranges.

File Structure:

1. Header Section:

   • Describes the overall file metadata.
   • Fixed size for simplicity.

2. Index Section:

   • Row Index
     • Maps rows to their corresponding data offsets in the file.

3. Data Section:

   • Row Data
     • Contains the actual sparse matrix data in a compressed Row Format. along with the column number

Detailed Layout

1. Header Section

Description: File identifiers and general fine info
Size: 40 bytes

Field	Type	Size (Bytes)	Description
Magic Number	ASCII	4	File identifier - CRAM
Version	Integer	2	File format version
Rows	Integer	4	Number of rows in the matrix
Columns	Integer	4	Number of columns in the matrix
Non-Zero Count	Integer	8	Total number of non-zero entries
Index Offset	Integer	8	Byte offset to the index section
Data Offset	Integer	8	Byte offset to the data section

2. Index Section

Description: Maps Rows to their corresponding data offsets
Size: 16 bytes

Field	Type	Size (Bytes)	Description
Row ID	Integer	4	Row ID
Offset	Integer	8	Byte offset in the data section
Non-Zero Count	Integer	4	Number of non-zero entries

3. Data Section

Description: Data elements of the
Size: 8

Field	Type	Size (Bytes)	Description
Column Index	Integer	4	Column index of the value
Value	Float	4	The matrix value

Installation

To install the package

pip install sparse-CRAM

Usage:

cram_path = '/path/to/cram_file.cram'
fileparser = CRAM.FileParser(cram_path)
headers = fileparser.parse_headers()