Description

Quickly check that input files appear to be intact. Checks that beginning of the file contains a valid header (all formats) containing at least one target sequence and then seeks to the end of the file and checks that an end-of-file (EOF) is present and intact (BAM and CRAM only). Alignment records are not checked. The quickcheck module returns a non-zero EXIT_CODE if any input files don't have a valid header or are missing an EOF block. Otherwise EXIT_CODE is zero.

Input

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Description
Pattern

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Output

Name
Description
Pattern

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Tools

samtools Documentation

Tools for dealing with SAM, BAM and CRAM files

https://github.com/samtools/doi: 10.1093/bioinformatics/btp352License: MIT
Authors