Bioinformatics

This page lists the safe and destructive patterns in the Sequence Tools shell guard pack. See Shell Tool for how these patterns are evaluated.

Sequence Tools

Pack ID: bioinformatics.sequence_tools

Guards against destructive bioinformatics sequence analysis operations

Rule ID	Pattern
`bioinformatics.sequence_tools.samtools_view`	`^samtools\s+view\b[^\|><]*$`
`bioinformatics.sequence_tools.samtools_flagstat`	`^samtools\s+flagstat\b[^\|><]*$`
`bioinformatics.sequence_tools.samtools_stats`	`^samtools\s+stats\b[^\|><]*$`
`bioinformatics.sequence_tools.samtools_idxstats`	`^samtools\s+idxstats\b[^\|><]*$`
`bioinformatics.sequence_tools.samtools_depth`	`^samtools\s+depth\b[^\|><]*$`
`bioinformatics.sequence_tools.bcftools_view`	`^bcftools\s+view\b[^\|><]*$`
`bioinformatics.sequence_tools.bcftools_query`	`^bcftools\s+query\b[^\|><]*$`
`bioinformatics.sequence_tools.bcftools_stats`	`^bcftools\s+stats\b[^\|><]*$`
`bioinformatics.sequence_tools.bedtools_intersect`	`^bedtools\s+intersect\b[^\|><]*$`
`bioinformatics.sequence_tools.bedtools_coverage`	`^bedtools\s+coverage\b[^\|><]*$`
`bioinformatics.sequence_tools.fastqc`	`^fastqc\b[^\|><]*$`
`bioinformatics.sequence_tools.multiqc`	`^multiqc\b[^\|><]*$`
`bioinformatics.sequence_tools.blastn`	`^blastn\b[^\|><]*$`
`bioinformatics.sequence_tools.blastp`	`^blastp\b[^\|><]*$`
`bioinformatics.sequence_tools.blastx`	`^blastx\b[^\|><]*$`
`bioinformatics.sequence_tools.feature_counts`	`^featureCounts\b[^\|><]*$`
`bioinformatics.sequence_tools.htseq_count`	`^htseq-count\b[^\|><]*$`

Rule ID	Reason	Suggestion	Confidence
`bioinformatics.sequence_tools.samtools_reheader`	Replaces BAM/CRAM header in-place, potentially corrupting alignment metadata	Backup the file first; verify the new header with `samtools view -H`	Medium
`bioinformatics.sequence_tools.bcftools_annotate_remove`	Removes annotations from VCF/BCF files, which may discard important variant metadata	Backup the VCF file first; review annotations with `bcftools query`	Medium
`bioinformatics.sequence_tools.bgzip_force`	Force-compresses files, overwriting existing .gz outputs without confirmation	Remove the `-f` flag; rename or backup existing compressed files first	Medium
`bioinformatics.sequence_tools.tabix_force`	Force-rebuilds index files, overwriting existing indices	Backup existing index files first	Medium