Table 1.
Descriptions of BAMQL connectives and predicates
| Category | Syntax | Description |
|---|---|---|
| Logical Connectives | ! expr | Is satisfied if expr is not satisfied. |
| expr | expr | Is satisfied if at least one operand is satisfied. | |
| expr ^ expr | Is satisfied if at exactly one operand is satisfied. | |
| expr & expr | Is satisfied only if both operands are satisfied. | |
| 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. |
| proper_pair? | The read is mapped in a proper pair | |
| unmapped? | The read is unmapped. | |
| mate_unmapped? | The mate is unmapped. | |
| mapped_to_reverse? | The read is mapped to the reverse strand. | |
| mate_mapped_to_reverse? | The mate is mapped to the reverse strand. | |
| raw_flag(int) | The read matches the specified SAM flag. | |
| read1? | The read is the first read in a pair. | |
| read2? | The read is the second read in a pair. | |
| secondary? | The alignment is not primary. | |
| failed_qc? | The read failed platform/vendor quality control checks. | |
| duplicate? | The read is either a PCR or optical duplicate | |
| supplementary? | The alignment is supplementary. | |
| Mapping Information | chr(glob) | The read is mapped to the specified chromosome. |
| mapping_quality(probability) | Matches the read if the proability of error is less than the specified probability. | |
| 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. |
| before(position) | Matches all reads that cover the specified position or any lower position. | |
| 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. |
| 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. | |
| random(probability) | The read is chosen based on a uniform pseudo-random variable. | |
| true | Always satisfied. | |
| false | Never satisfied. |