Feature: MAF slicing In order to obtain just the alignment data covering a given region I want to be able to take slices of alignment blocks over A given interval

Scenario: Interval covering two blocks Given a MAF source file "mm8_chr7_tiny.maf" And a Kyoto Cabinet index file "mm8_chr7_tiny.kct" When I open it with a MAF reader And I enable the :remove_gaps parser option And open a new MAF writer And write the header from the original MAF file And filter for only the species | mm8 | | rn4 | And search for blocks between positions 80082350 and 80082380 of mm8.chr7 And slice the resulting blocks according to the given interval And write all the matched blocks Then the output should match, except whitespace, "mm8_chr7_tiny_slice1.maf"

Scenario: Interval covering two blocks, using directory access, counting Given indexed MAF files in "test/data" When I enable the :remove_gaps parser option And filter for only the species | mm8 | | rn4 | And I extract a slice over the genomic interval | chrom | start | end | | mm8.chr7 | 80082350 | 80082380 | Then 2 blocks are obtained

Scenario: Interval covering two blocks, using directory access Given indexed MAF files in "test/data" When I enable the :remove_gaps parser option And open a new MAF writer And write a default header And filter for only the species | mm8 | | rn4 | And I extract a slice over the genomic interval | chrom | start | end | | mm8.chr7 | 80082350 | 80082380 | And write all the matched blocks Then the output should match, except whitespace, "mm8_chr7_tiny_slice1.maf"

Scenario: Interval in block subset Given indexed MAF files in "test/data" When I open a new MAF writer And write a default header And I extract a slice over the genomic interval | chrom | start | end | | mm8.chr7 | 80082718 | 80082728 | And write all the matched blocks Then the output should match, except whitespace, "mm8_chr7_tiny_slice2.maf"

Scenario: Interval to end of block Given indexed MAF files in "test/data" When I open a new MAF writer And write a default header And I extract a slice over the genomic interval | chrom | start | end | | mm8.chr7 | 80082757 | 80082767 | And write all the matched blocks Then the output should match, except whitespace, "mm8_chr7_tiny_slice3.maf"