transrate 1.0.0.alpha.4 → 1.0.0.alpha.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 2f7b1950319885f1e22e62ea5def9d44c2bf50c8
-  data.tar.gz: 2a0fc6c4ad1a23be8ea560f63d2f4c8af144b35f
+  metadata.gz: 3fc633cd9166010a55ea892edc4737c2f3221ccf
+  data.tar.gz: 2e9729a73f4128503d992b39c9711e15c89bae7b
 SHA512:
-  metadata.gz: 837907dea75820b5e6630a2db91bff70cd8c1cdd00ce14dd450e298ed301dc0a593c726b11e5abd6a48e72aadfd8e8aeec98c62571dd6a11a1d3494657b309b1
-  data.tar.gz: f8eec588917af4737fe49482c2c8e6bfbf281a1531fde7be5f4956f68bf16a0d07f2ef5bf67aefe7b4b0b3697bd47ab36734cee4e9708666d15f2247c9b4e8e0
+  metadata.gz: ef6f9cc4be67ec2b5d09fc9ab7487e3b21b0409e0af63752f33cf977e1d3f50f1644622af76cfba54d6b28c63b36a3607842d38ce0fdec51ff6c4d67063b571f
+  data.tar.gz: d4cc715ba05d3a332882a492fd99ea4ad79f48198dce550b7c1cefed3025663ff88ed7257554e9f4897fbb20f23c337135d72e6a8f3ac142182162875ff6dafa

data/lib/transrate/contig.rb

@@ -231,18 +231,16 @@ module Transrate
       (length - low_uniqueness_bases) / length.to_f
     end
 
-    # Contig score (geometric mean of all score components)
+    # Contig score (product of all score components)
     def score
       return @score if @score != -1
       prod =
-        [p_bases_covered, 0.01].max * # proportion of bases covered
-        [p_not_segmented, 0.01].max * # prob contig has 0 changepoints
-        [p_good, 0.01].max * # proportion of reads that mapped good
-        [p_seq_true, 0.01].max * # scaled 1 - mean per-base edit distance
-        [p_unique, 0.01].max # prop mapQ >= 5
-      s = prod ** (1.0 / 5)
-      s = 0.01 if !s
-      @score = [s, 0.01].max
+        [p_bases_covered, 0.01].max.to_f * # proportion of bases covered
+        [p_not_segmented, 0.01].max.to_f * # prob contig has 0 changepoints
+        [p_good, 0.01].max.to_f * # proportion of reads that mapped good
+        [p_seq_true, 0.01].max.to_f * # scaled 1 - mean per-base edit distance
+        [p_unique, 0.01].max.to_f # prop mapQ >= 5
+      @score = [prod, 0.01].max
     end
   end
 

data/lib/transrate/samtools.rb

@@ -23,8 +23,9 @@ module Transrate
       runcmd = Cmd.new "#{Samtools.path} #{cmd}"
       runcmd.run
       if !runcmd.status.success?
-        logger.warn "Samtools command failed: #{runcmd}" +
-                    "\n#{runcmd.stderr}"
+        raise SamtoolsError.new("Samtools command failed: #{runcmd}" +
+                                "\n#{runcmd.stderr}" +
+                                "\n#{runcmd.stdout}")
       end
       runcmd.stdout
     end

data/lib/transrate/snap.rb

@@ -58,7 +58,7 @@ module Transrate
         runner.run
         save_readcount runner.stdout
         unless runner.status.success?
-          raise SnapError.new("Snap failed\n#{runner.stderr}")
+          raise SnapError.new("Snap failed\n#{runner.stderr}\n#{runner.stdout}")
         end
       else
         load_readcount left

data/lib/transrate/version.rb

@@ -11,7 +11,7 @@ module Transrate
     MAJOR = 1
     MINOR = 0
     PATCH = 0
-    BUILD = 'alpha.4'
+    BUILD = 'alpha.5'
 
     STRING = [MAJOR, MINOR, PATCH, BUILD].compact.join('.')
   end

data/test/test_read_metrics.rb

@@ -43,7 +43,7 @@ class TestReadMetrics < Test::Unit::TestCase
           assert_equal 2, stats[:contigs_uncovbase], 'uncovered base contig'
           assert_equal 0, stats[:contigs_uncovered], 'uncovered contig'
           assert_equal 0, stats[:contigs_lowcovered], 'lowcovered contig'
-          assert_equal 2, stats[:contigs_good], 'good contigs'
+          assert_equal 0, stats[:contigs_good], 'good contigs'
         end
       end
     end

data/test/test_transrater.rb

@@ -59,7 +59,7 @@ class TestTransrater < Test::Unit::TestCase
         Dir.chdir tmpdir do
           all = @rater.all_metrics(@left, @right)
           score = @rater.assembly_score
-          assert_equal 0.40908, score.round(5) # regression test
+          assert_equal 0.10231, score.round(5) # regression test
         end
       end
     end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: transrate
 version: !ruby/object:Gem::Version
-  version: 1.0.0.alpha.4
+  version: 1.0.0.alpha.5
 platform: ruby
 authors:
 - Richard Smith-Unna
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-10-21 00:00:00.000000000 Z
+date: 2014-10-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: yell