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Versions: 9
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Contents
Feature: Provide access to multiple MAF files in a directory
In order to efficiently work with many MAF files
We need to provide a convenient interface to them
Scenario: Query for several chromosomes at once
Given indexed MAF files in "test/data"
When I query for the genomic intervals
| chrom | start | end |
| mm8.chr7 | 80082580 | 80082612 |
| mm8.chrM | 1400 | 1590 |
Then 5 blocks are obtained
Scenario: Apply block filters
Given indexed MAF files in "test/data"
When I filter for blocks with text size at most 200
And I query for the genomic intervals
| chrom | start | end |
| mm8.chr7 | 80082580 | 80082612 |
| mm8.chrM | 1400 | 1590 |
Then 3 blocks are obtained
Scenario: Apply sequence filters
Given indexed MAF files in "test/data"
When I filter for only the species
| mm8 |
| rn4 |
| hg18 |
And I query for the genomic intervals
| chrom | start | end |
| mm8.chr7 | 80082580 | 80082612 |
| mm8.chrM | 1400 | 1590 |
Then 5 blocks are obtained
And block 0 has 3 sequences
Scenario: Set parse options
Given indexed MAF files in "test/data"
When I enable the :remove_gaps parser option
And I filter for only the species
| mm8 |
| rn4 |
| hg18 |
And I query for the genomic intervals
| chrom | start | end |
| mm8.chr7 | 80082580 | 80082612 |
Then 2 blocks are obtained
And the text size of block 1 is 121
Version data entries
9 entries across 9 versions & 1 rubygems