Feature: Remove gaps from MAF files In order to work with only the alignment data involving sequences Which can be used by downstream software We may want to filter out certain species Which can leave gap regions where sequence data was only present For removed species So it is useful to be able to remove those gaps

Background: Given MAF data: """ ##maf version=1 a score=10542.0 s mm8.chr7 80082334 34 + 145134094 GGGCTGAGGGC--AGGGATGG---AGGGCGGTCC--------------CAGCA- s rn4.chr1 136011785 34 + 267910886 GGGCTGAGGGC--AGGGACGG---AGGGCGGTCC--------------CAGCA- s oryCun1.scaffold_199771 14021 43 - 75077 -----ATGGGC--AAGCGTGG---AGGGGAACCTCTCCTCCCCTCCGACAAAG- s hg18.chr15 88557580 27 + 100338915 --------GGC--AAGTGTGGA--AGGGAAGCCC--------------CAGAA- s panTro2.chr15 87959837 27 + 100063422 --------GGC--AAGTGTGGA--AGGGAAGCCC--------------CAGAA- s rheMac2.chr7 69864714 28 + 169801366 -------GGGC--AAGTATGGA--AGGGAAGCCC--------------CAGAA- s canFam2.chr3 56030570 39 + 94715083 AGGTTTAGGGCAGAGGGATGAAGGAGGAGAATCC--------------CTATG- s dasNov1.scaffold_106893 7435 34 + 9831 GGAACGAGGGC--ATGTGTGG---AGGGGGCTGC--------------CCACA- s loxAfr1.scaffold_8298 30264 38 + 78952 ATGATGAGGGG--AAGCGTGGAGGAGGGGAACCC--------------CTAGGA s echTel1.scaffold_304651 594 37 - 10007 -TGCTATGGCT--TTGTGTCTAGGAGGGGAATCC--------------CCAGGA """ When I open it with a MAF reader And filter for only the species | mm8 | | rn4 | | hg18 | | canFam2 | | loxAfr1 |

Scenario: Detect filtered blocks When an alignment block can be obtained Then the alignment block is marked as filtered And the alignment block has 5 sequences

Scenario: Detect gaps When an alignment block can be obtained Then 1 gap is found with length [14]

Scenario: Remove gaps When an alignment block can be obtained And gaps are removed Then the text size of the block is 40

Scenario: Remove gaps in the parser When I enable the :remove_gaps parser option And an alignment block can be obtained Then the text size of the block is 40