rbbt-util 5.17.30 → 5.17.31

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: dd71175671c8e61af5f2149e9f191bb207169112
-  data.tar.gz: 4ee95675d9f232f82b7e918bc3a6b0cd0f47cbd7
+  metadata.gz: ec2769ac8dcfb78a8e3b33cdf905f2b0e53e9340
+  data.tar.gz: 9362e1f40b97de7451f0f4ed7467a7f386745128
 SHA512:
-  metadata.gz: fa1772442429aab7a19e5fb2d7af81ed73c22fe41ba0397524eb2ba373c07fcf87023efa1de73b0dcb23a91276f1ad3aee4bd25c776fd77d8f54b4409256502d
-  data.tar.gz: 1dc00f98b9eb0c901787569308b681e54996e95862d7129db6ffdc345921fc81b511f50bce10c0090661ac4eebc0be19f2b86183d446769f2b557de9285175f3
+  metadata.gz: 5df33607c693b25c3a0ff547ef690be714f2fa568fb9fd2f8d39819cd6ab8166fbd69cc5f212f5514460693190f349c4c699215c786b9ddcf3d546805dff174b
+  data.tar.gz: 53fdcaded28ebccbe7f88335e3448046300698554deba0bcf3e44b478ea131229128c2b2460f8db18e0ad3f67d83c425020c89bb22013c707a2c377a281937f2

data/lib/rbbt/tsv/parallel/traverse.rb

@@ -29,20 +29,19 @@ module TSV
       when Array, Hash
         obj.size
       when File
-        return nil if Misc.gzip?(file) or Misc.bgzip?(file)
+        return nil if Open.gzip?(file) or Open.bgzip?(file)
         CMD.cmd("wc -l '#{obj.filename}'").read.to_i
-      when Path
-        return nil if Misc.gzip?(file) or Misc.bgzip?(file)
-        CMD.cmd("wc -l '#{obj.find}'").read.to_i
-      when String
+      when Path, String
+        obj = obj.find if Path === obj
         if File.exists? obj
-          return nil if Misc.gzip?(file) or Misc.bgzip?(file)
+          return nil if Open.gzip?(obj) or Open.bgzip?(obj)
           CMD.cmd("wc -l '#{obj}'").read.to_i
         else
           nil
         end
       end
     rescue Exception
+      Log.exception $!
       nil
     end
   end

data/lib/rbbt/util/misc/omics.rb

@@ -197,16 +197,35 @@ module Misc
     line = io.gets.strip
     parts = line.split(sep)
     chr, start, eend, *rest = parts
-    [line,chr, start.to_i, eend.to_i, rest]
+    start = start.to_i
+    if eend =~ /^\d+$/
+      eend = eend.to_i
+    else
+      eend = start.to_i
+    end
+    [line,chr, start, eend, rest]
+  end
+
+  def self.intersect_streams_cmp_chr(chr1, chr2)
+    return chr1 <=> chr2
+    if chr1 =~ /^\d+$/ and chr2 =~ /^\d+$/
+      chr1 <=> chr2
+    elsif chr1 =~ /^\d+$/
+      -1
+    elsif chr2 =~ /^\d+$/
+      1
+    else
+      chr1 <=> chr2
+    end
   end
 
   def self.intersect_streams(f1, f2, out, sep=":")
     finish = false
     line1, chr1, start1, eend1, rest1 = intersect_streams_read(f1,sep)
     line2, chr2, start2, eend2, rest2 = intersect_streams_read(f2,sep)
-    Misc.profile do
     while not finish
-      case chr1 <=> chr2
+      cmp = intersect_streams_cmp_chr(chr1,chr2)
+      case cmp
       when -1
         move = 1
       when 1
@@ -249,6 +268,11 @@ module Misc
         end
       end
     end
+  end
+
+  def self.select_ranges(stream1, stream2, sep = "\t")
+    Misc.open_pipe do |sin|
+      intersect_streams(stream1, stream2,sin, sep)
     end
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.17.30
+  version: 5.17.31
 platform: ruby
 authors:
 - Miguel Vazquez