From dc9e4098b2f6d71a5fc13f998443122f679b7302 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 25 Aug 2010 15:42:02 +0000
Subject: [PATCH] accidentally commited an old tool

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4109 348d0f76-0448-11de-a6fe-93d51630548a
---
 ruby/index/diffIndexes.rb | 170 --------------------------------------
 1 file changed, 170 deletions(-)
 delete mode 100644 ruby/index/diffIndexes.rb

diff --git a/ruby/index/diffIndexes.rb b/ruby/index/diffIndexes.rb
deleted file mode 100644
index 7ec0414fa..000000000
--- a/ruby/index/diffIndexes.rb
+++ /dev/null
@@ -1,170 +0,0 @@
-# this ruby files takes two indexes (of the same type) and diff's them.  If they're different types,
-# it'll stop after the header
-
-# a function to exit, printing a message
-def exitWithError(message) 
-	puts ###########################################
-	puts message
-	puts ###########################################
-	exit(1)
-end
-
-
-if (ARGV.size != 2)
-	exitWithError("We take two files as input, try again!")	
-end
-
-# open the indexes
-index1 = File.new(ARGV[0])
-index2 = File.new(ARGV[1])
-
-# a helper function for comparing values
-def compValues(file1, file2, byteCount, type)
-	index1Type = file1.sysread(byteCount)
-	index2Type = file2.sysread(byteCount)
-	if (index1Type != index2Type)
-		print "#{type}, index1 (#{index1Type}) != index2 (#{index2Type})\n"
-	else 
-		print "#{type}, index1 (#{index1Type}) == index2 (#{index2Type})\n"
-	end
-end
-
-# a helper function for comparing values
-def compInts(file1, file2, byteCount, type)
-	if (byteCount > 4) 
-		upack = "q"
-	else 
-		upack = "i"
-	end
-	index1Type = file1.sysread(byteCount).unpack(upack)
-	index2Type = file2.sysread(byteCount).unpack(upack)
-	if (index1Type != index2Type)
-		print "#{type}, index1 (#{index1Type}) != index2 (#{index2Type})\n"
-	else 
-		print "#{type}, index1 (#{index1Type}) == index2 (#{index2Type})\n"
-	end
-end
-
-
-# a helper function for reading strings
-def readString(index)
-	buffer = []
-	ch = index.sysread(1)
-	while (ch != "\0")
-		buffer.push(ch)
-		ch = index.sysread(1)
-	end
-	buffer.to_s
-end
-
-# validate the magic number from both
-exitWithError("Magic number not valid for index 1") if index1.sysread(4) != "TIDX"
-exitWithError("Magic number not valid for index 2") if index2.sysread(4) != "TIDX"
-
-# validate the types
-compInts(index1,index2,4,"types")
-
-# validate the versions
-v1 = index1.sysread(4).unpack("i")
-v2 = index2.sysread(4).unpack("i")
-if (v1 != v2)
-	print "version, index1 (#{v1}) != index2 (#{v2})\n"
-else 
-	print "version, index1 (#{v1}) == index2 (#{v2})\n"
-end
-
-# validate the filenames
-fl1 = readString(index1)
-fl2 = readString(index2)
-if (fl1 != fl2)
-	print "filename, index1 (#{fl1}) != index2 (#{fl2})\n"
-else 
-	print "filename, index1 (#{fl1}) == index2 (#{fl2})\n"
-end
-# validate the sizes
-compInts(index1,index2,8,"sizes")
-
-
-# validate the T5?
-compValues(index1,index2,8,"T5")
-
-# validate the MD5 - just a byte, we don't write the MD5 sums in yet
-# validate the filenames
-fl1 = readString(index1)
-fl2 = readString(index2)
-if (fl1 != fl2)
-	print "md5, index1 (#{fl1}) != index2 (#{fl2})\n"
-else 
-	print "md5, index1 (#{fl1}) == index2 (#{fl2})\n"
-end
-
-# validate the flags
-index1Flags = (index1.sysread(4)).unpack("L")
-index2Flags = (index2.sysread(4)).unpack("L")
-if (index1Flags != index2Flags)
-		print "Flags are different, index1 = #{index1Flags[0]}, index2 = #{index2Flags[0]}\n"
-end
-		
-def readSeqDictionary(file)
-	puts "reading seq dict"
-	sequences = []
-	count = (file.sysread(4)).unpack("i")	
-	puts count
-	count[0].times {|index|
-		sequences.add(readString(file).to_s)
-		file.sysread(4) # drop the sizes for now
-	}
-	sequences # return sequences
-end
-
-if (index1Flags[0] == 32768)
-	puts readSeqDictionary(index1)
-elsif (index2Flags[0] == 32768)
-	puts readSeqDictionary(index2)
-end
-
-# bump off the prop dictionary
-index1.sysread(4) if (v1[0] == 3) 
-index2.sysread(4) if (v2[0] == 3) 
-
-def readSeqEntry(i1)
-    puts "--------------------------------------------" 
-	puts "Contig --> #{readString(i1).to_s}"
-	print "bin width         = #{(i1.sysread(4)).unpack("i")}\n"
-	binCount = (i1.sysread(4)).unpack("i")[0]
-	print "number of bins    = #{binCount}\n"		
-	print "longest feature   = #{(i1.sysread(4)).unpack("i")}\n"
-	print "max bin size      = #{(i1.sysread(4)).unpack("i")}\n"
-	print "total bin size    = #{(i1.sysread(4)).unpack("i")}\n"
-	lastStartPos = -1
-	binCount.times { |index|
-		startPos = (i1.sysread(8)).unpack("q")[0]	
-		#if (startPos < lastStartPos)
-			puts "bin at index #{index}, this start = #{startPos}, last start = #{lastStartPos}"
-		#end
-		lastStartPos = startPos
-	}
-		
-end
-
-def compContigLinear(i1, i2)
-	seqC1 = (i1.sysread(4)).unpack("L")
-	seqC2 = (i2.sysread(4)).unpack("L")	
-	print "seq count 1 = #{seqC1}, count 2 = #{seqC2}\n"
-	puts "\nentries for index 1"
-	seqC1[0].times { |index|
-		readSeqEntry(i1)			
-	} 
-	puts "\nentries for index 2"	
-	seqC2[0].times { |index|
-		readSeqEntry(i2)	
-	} 
-end
-
-compContigLinear(index1,index2)		
-	
-
-print "Done!\n"
-# close the files
-index1.close()
-index2.close()
\ No newline at end of file