finishm 0.0.8 → 0.0.9

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: finishm
 version: !ruby/object:Gem::Version
-  version: 0.0.8
+  version: 0.0.9
 platform: ruby
 authors:
 - Ben J. Woodcroft
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-08-01 00:00:00.000000000 Z
+date: 2016-08-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-ipcress
@@ -416,7 +416,6 @@ files:
 - ext/src/third-party/zlib-1.2.3/Makefile.in
 - ext/src/third-party/zlib-1.2.3/README
 - ext/src/third-party/zlib-1.2.3/adler32.c
-- ext/src/third-party/zlib-1.2.3/adler32.o
 - ext/src/third-party/zlib-1.2.3/algorithm.txt
 - ext/src/third-party/zlib-1.2.3/amiga/Makefile.pup
 - ext/src/third-party/zlib-1.2.3/amiga/Makefile.sas
@@ -425,7 +424,6 @@ files:
 - ext/src/third-party/zlib-1.2.3/as400/readme.txt
 - ext/src/third-party/zlib-1.2.3/as400/zlib.inc
 - ext/src/third-party/zlib-1.2.3/compress.c
-- ext/src/third-party/zlib-1.2.3/compress.o
 - ext/src/third-party/zlib-1.2.3/configure
 - ext/src/third-party/zlib-1.2.3/contrib/README.contrib
 - ext/src/third-party/zlib-1.2.3/contrib/ada/buffer_demo.adb
@@ -553,11 +551,8 @@ files:
 - ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.vcproj
 - ext/src/third-party/zlib-1.2.3/crc32.c
 - ext/src/third-party/zlib-1.2.3/crc32.h
-- ext/src/third-party/zlib-1.2.3/crc32.o
 - ext/src/third-party/zlib-1.2.3/deflate.c
 - ext/src/third-party/zlib-1.2.3/deflate.h
-- ext/src/third-party/zlib-1.2.3/deflate.o
-- ext/src/third-party/zlib-1.2.3/example
 - ext/src/third-party/zlib-1.2.3/example.c
 - ext/src/third-party/zlib-1.2.3/examples/README.examples
 - ext/src/third-party/zlib-1.2.3/examples/fitblk.c
@@ -570,22 +565,15 @@ files:
 - ext/src/third-party/zlib-1.2.3/examples/zpipe.c
 - ext/src/third-party/zlib-1.2.3/examples/zran.c
 - ext/src/third-party/zlib-1.2.3/gzio.c
-- ext/src/third-party/zlib-1.2.3/gzio.o
 - ext/src/third-party/zlib-1.2.3/infback.c
-- ext/src/third-party/zlib-1.2.3/infback.o
 - ext/src/third-party/zlib-1.2.3/inffast.c
 - ext/src/third-party/zlib-1.2.3/inffast.h
-- ext/src/third-party/zlib-1.2.3/inffast.o
 - ext/src/third-party/zlib-1.2.3/inffixed.h
 - ext/src/third-party/zlib-1.2.3/inflate.c
 - ext/src/third-party/zlib-1.2.3/inflate.h
-- ext/src/third-party/zlib-1.2.3/inflate.o
 - ext/src/third-party/zlib-1.2.3/inftrees.c
 - ext/src/third-party/zlib-1.2.3/inftrees.h
-- ext/src/third-party/zlib-1.2.3/inftrees.o
-- ext/src/third-party/zlib-1.2.3/libz.a
 - ext/src/third-party/zlib-1.2.3/make_vms.com
-- ext/src/third-party/zlib-1.2.3/minigzip
 - ext/src/third-party/zlib-1.2.3/minigzip.c
 - ext/src/third-party/zlib-1.2.3/msdos/Makefile.bor
 - ext/src/third-party/zlib-1.2.3/msdos/Makefile.dj2
@@ -608,9 +596,7 @@ files:
 - ext/src/third-party/zlib-1.2.3/qnx/package.qpg
 - ext/src/third-party/zlib-1.2.3/trees.c
 - ext/src/third-party/zlib-1.2.3/trees.h
-- ext/src/third-party/zlib-1.2.3/trees.o
 - ext/src/third-party/zlib-1.2.3/uncompr.c
-- ext/src/third-party/zlib-1.2.3/uncompr.o
 - ext/src/third-party/zlib-1.2.3/win32/DLL_FAQ.txt
 - ext/src/third-party/zlib-1.2.3/win32/Makefile.bor
 - ext/src/third-party/zlib-1.2.3/win32/Makefile.emx
@@ -625,7 +611,6 @@ files:
 - ext/src/third-party/zlib-1.2.3/zlib.h
 - ext/src/third-party/zlib-1.2.3/zutil.c
 - ext/src/third-party/zlib-1.2.3/zutil.h
-- ext/src/third-party/zlib-1.2.3/zutil.o
 - finishm.gemspec
 - lib/assembly/a_b_visualiser.rb
 - lib/assembly/acyclic_connection_finder.rb
@@ -662,6 +647,7 @@ files:
 - lib/assembly/velvet_graph_sequence_extractor.rb
 - lib/external/VERSION
 - lib/finishm/assemble.rb
+- lib/finishm/connect.rb
 - lib/finishm/explore.rb
 - lib/finishm/finisher.rb
 - lib/finishm/fluff.rb
@@ -761,9 +747,22 @@ files:
 - spec/data/gapfilling/4/HOWTO_recreate
 - spec/data/gapfilling/4/reads.fa.gz
 - spec/data/gapfilling/5/HOWTO_RECREATE
+- spec/data/gapfilling/5/a.svg
 - spec/data/gapfilling/5/answer.fna
 - spec/data/gapfilling/5/gappy.fna
 - spec/data/gapfilling/5/reads.fa
+- spec/data/gapfilling/5/reads.faVanswer.bam
+- spec/data/gapfilling/5/reads.faVanswer.bam.bai
+- spec/data/gapfilling/5/reads2.fa
+- spec/data/gapfilling/5/to_gapfill.fa
+- spec/data/gapfilling/5/velvet23_3.5/Graph2
+- spec/data/gapfilling/5/velvet23_3.5/LastGraph
+- spec/data/gapfilling/5/velvet23_3.5/Log
+- spec/data/gapfilling/5/velvet23_3.5/PreGraph
+- spec/data/gapfilling/5/velvet23_3.5/Roadmaps
+- spec/data/gapfilling/5/velvet23_3.5/Sequences
+- spec/data/gapfilling/5/velvet23_3.5/contigs.fa
+- spec/data/gapfilling/5/velvet23_3.5/stats.txt
 - spec/data/gapfilling/5/velvet51_3.5/LastGraph
 - spec/data/gapfilling/5/velvet51_3.5/Sequences
 - spec/data/gapfilling/6/random1.fa
@@ -823,12 +822,16 @@ files:
 - spec/data/velvet_test_trails_reverse/reads_reversed.fa
 - spec/data/visualise/1/LastGraph
 - spec/data/visualise/2_paired_end/HOWTO_RECREATE.txt
+- spec/data/visualise/2_paired_end/a.svg
 - spec/data/visualise/2_paired_end/rand1.fa
 - spec/data/visualise/2_paired_end/rand2.fa
 - spec/data/visualise/2_paired_end/with_gaps.fa
 - spec/data/visualise/2_paired_end/with_gaps.read_pairs.fa.gz
 - spec/data/wander/1/random1.fa
 - spec/data/wander/1/random1.sammy.fa
+- spec/data/wander/1/reference.broken.fa
+- spec/data/wander/1/reference.fa
+- spec/data/wander/1/reference_reads.fa
 - spec/depth_first_search_spec.rb
 - spec/dijkstra_spec.rb
 - spec/explore_spec.rb
@@ -863,7 +866,7 @@ files:
 - validation/gapfill_simulate_perfect.rb
 homepage: http://github.com/wwood/finishm
 licenses:
-- GPL3+
+- GPL-3.0+
 metadata: {}
 post_install_message: 
 rdoc_options: []
@@ -871,9 +874,9 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - "~>"
     - !ruby/object:Gem::Version
-      version: '0'
+      version: '2.3'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="