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