Table 1 Descriptions of BAMQL connectives and predicates
From: BAMQL: a query language for extracting reads from BAM files
Category | Syntax | Description |
|---|---|---|
Logical Connectives | ! expr | Is satisfied if expr is not satisfied. |
| Â | expr | expr | Is satisfied if at least one operand is satisfied. |
| Â | expr ^ expr | Is satisfied if at exactly one operand is satisfied. |
| Â | expr & expr | Is satisfied only if both operands are satisfied. |
| Â | cond then then_expr else else_expr | If cond is satisfied, this expression will only be satisfied if then_expr is satisfied. If cond is not satisfied, then this expression will only be satisfied if else_expression is satisfied. |
BAM Flags | paired? | The read is paired in sequencing. |
| Â | proper_pair? | The read is mapped in a proper pair |
| Â | unmapped? | The read is unmapped. |
| Â | mate_unmapped? | The mate is unmapped. |
| Â | mapped_to_reverse? | The read is mapped to the reverse strand. |
| Â | mate_mapped_to_reverse? | The mate is mapped to the reverse strand. |
| Â | raw_flag(int) | The read matches the specified SAM flag. |
| Â | read1? | The read is the first read in a pair. |
| Â | read2? | The read is the second read in a pair. |
| Â | secondary? | The alignment is not primary. |
| Â | failed_qc? | The read failed platform/vendor quality control checks. |
| Â | duplicate? | The read is either a PCR or optical duplicate |
| Â | supplementary? | The alignment is supplementary. |
Mapping Information | chr(glob) | The read is mapped to the specified chromosome. |
| Â | mapping_quality(probability) | Matches the read if the proability of error is less than the specified probability. |
| Â | mate_chr(glob) | The mate is mapped to the specified chromosome. |
|  | split_pair? | Matches if both the read and it’s mate pair are mapped, but only if to different chromosomes. |
Position | after(position) | Matches all reads that cover the specified position or any higher position. |
| Â | before(position) | Matches all reads that cover the specified position or any lower position. |
| Â | position(start,end) | Matches all sequences that cover the range of position from specified start to end, i.e. N matches any base. |
Sequence | nt(position,n) | Matches all reads that are classified as the IUPAC-style nucleotide n at the specified position, i.e. N matches N. |
| Â | nt_exact(position,n) | Matches all reads that exactly match the IUPAC-style nucleotide n at the specified position. |
Miscellaneous | read_group(glob) | Matches the read group. |
|  | header ~ /regex/ | Matches a Perl-compatible regular expression against the read’s header. |
| Â | random(probability) | The read is chosen based on a uniform pseudo-random variable. |
| Â | true | Always satisfied. |
| Â | false | Never satisfied. |