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"