Compression and decompression reduction method and system for CIGAR domain of SAM and BAM files and medium

Abstract

The invention discloses an SAM and BAM file CIGAR domain compression and decompression reduction method and system, and a medium. The method comprises the following steps: coding CIGAR domain data ofan operator into a first specified content from the preprocessing before compression, and skipping to execute the step A6); encoding the CIGAR domain data of the two operators into second specified content only accommodating one operator and a digital part of the operator; cIGAR domain data coding of three or more operators omits a first operator M and a digital part ''\ d + M'' thereof, and the operator M of the last operator obtains a third specified content; preprocessing is carried out by combining the characteristics of a CIGAR domain; therefore, the content of the CIGAR domain can be preprocessed according to a certain rule to achieve high-power compression of the CIGAR domain, and the method has the advantages of being efficient and rapid in preprocessing, high in compression ratioand good in compression effect, can be suitable for two formats of SAM files and BAM files and has the advantage of being wide in application range.

Description

technical field [0001] The invention relates to the compression and restoration technology of SAM and BAM data in the field of biological information, in particular to a method, system and medium for compression, decompression and restoration of the CIGAR domain of SAM and BAM files. Background technique [0002] In bioinformatics, especially in the analysis of high-throughput sequencing data, most of the operations are to realize the comparison (mapping) of short fragment sequences and reference sequences, such as bwa, bowtie, etc., so a unified format needs to be used to Indicates the problem of this mapping result. The SAM (Sequence Alignment Map) file format is to solve this problem. It is a file format used to store the alignment results of sequencing reads and reference sequences. It uses TAB as a separator and supports short reads and long reads on different platforms. reads (up to 128Mbp). However, because the size of the SAM file is usually large, it will be conve...

AI Technical Summary

Problems solved by technology

However, the compression of the sixth field, the CIGAR domain, is still often not paid attention to at present, or the common compression method is used, resulting in a large optimization space for the compression of the CIGAR domain.

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