Table 2 Comparison of the error messages of the different tools for a syntax error involving a misplaced parenthesis
From: SamQL: a structured query language and filtering tool for the SAM/BAM file format
Tool | Syntax | Error message |
|---|---|---|
samql | (POS > 1 AND) (RNAME = "chr1") | Filter creation from where clause failed: found), expected identifier, string, number, bool at line 1, char 12 |
samtools | (pos > 1 &) (rname =  = "chr1") | Couldn't process filter expression |
sambamba | (position > 1 and) (ref_id =  = 0) | Parsing error near line 1: expected prefix operator |