@milestone_2 Feature: Indexed access to MAF files In order to extract alignment blocks from MAF files By chromosomal ranges matching a source sequence I want to have a way to build indexes on MAF files And use indexes to efficiently find alignment blocks Because linear searches of a 200 GB file are impractical

Scenario: Index a MAF file Given a MAF source file "mm8_chr7_tiny.maf" When I open it with a MAF reader And build an index on the reference sequence Then the index has at least 8 entries

Scenario: Extract alignment blocks by chromosomal range Given a MAF source file "mm8_chr7_tiny.maf" When I open it with a MAF reader And build an index on the reference sequence And search for blocks between positions 80082592 and 80082766 of mm8.chr7 Then 2 blocks are obtained And sequence mm8.chr7 of block 0 has start 80082592 And sequence mm8.chr7 of block 1 has start 80082713

Scenario: Extract alignment blocks by chromosomal range from index file 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 search for blocks between positions 80082592 and 80082766 of mm8.chr7 Then 2 blocks are obtained And sequence mm8.chr7 of block 0 has start 80082592 And sequence mm8.chr7 of block 1 has start 80082713

Scenario: Extract alignment blocks by chromosomal range on non-ref sequence Given a MAF source file "mm8_chr7_tiny.maf" When I open it with a MAF reader And build an index on all sequences And search for blocks between positions 136011819 and 136012026 of rn4.chr1 Then 2 blocks are obtained And sequence mm8.chr7 of block 0 has start 80082368 And sequence mm8.chr7 of block 1 has start 80082471

Scenario: Index MAF file with extended bin positions Given a MAF source file "ext-bin.maf" When I open it with a MAF reader And build an index on all sequences Then the index has at least 18 entries

@no_jruby Scenario: Build MAF index with CLI tool Given test files: | mm8_chr7_tiny.maf | When I run maf_index mm8_chr7_tiny.maf mm8_chr7_tiny.kct Then it should pass with: """ """ And a file named "mm8_chr7_tiny.kct" should exist

@no_jruby Scenario: Build MAF index on BGZF file with CLI tool Given test files: | mm8.chrM.maf.bgz | When I run maf_index mm8.chrM.maf.bgz mm8.chrM.kct Then it should pass with: """ """ And a file named "mm8.chrM.kct" should exist

@no_jruby Scenario: Build MAF index on all sequences with CLI tool Given test files: | mm8_chr7_tiny.maf | When I run maf_index --all mm8_chr7_tiny.maf mm8_chr7_tiny.kct And I run maf_index -d mm8_chr7_tiny.kct Then it should pass with regex: """ 9 [bin 585] 594:631 """

@no_jruby Scenario: Dump MAF index with CLI tool Given test files: | mm8_chr7_tiny.maf | | mm8_chr7_tiny.kct | When I run maf_index -d mm8_chr7_tiny.kct Then it should pass with regex: """ 0 [bin 1195] 80082334:80082368 """