Feature: MAF output In order to output modified MAF files or subsets of them I want to be able to write out parsed MAF data

Scenario: Reproduce simple test data Given a MAF source file "mm8_single.maf" When I open it with a MAF reader And open a new MAF writer And write the header from the original MAF file And write all the parsed blocks Then the output should match, except whitespace, "mm8_single.maf"

Scenario: Reproduce longer test data Given a MAF source file "mm8_chr7_tiny.maf" When I open it with a MAF reader And open a new MAF writer And write the header from the original MAF file And write all the parsed blocks Then the output should match, except whitespace, "mm8_chr7_tiny.maf"

Scenario: Reproduce test data with i, e, q lines Given a MAF source file "chr22_ieq.maf" When I enable the :parse_extended parser option And I enable the :parse_empty parser option And I open it with a MAF reader And open a new MAF writer And write the header from the original MAF file And write all the parsed blocks Then the output should match, except whitespace, "chr22_ieq.maf"