accidentally commited an old tool
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4109 348d0f76-0448-11de-a6fe-93d51630548a
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aaron
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bc0826801c
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dc9e4098b2
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@ -1,170 +0,0 @@
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# this ruby files takes two indexes (of the same type) and diff's them. If they're different types,
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# it'll stop after the header
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# a function to exit, printing a message
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def exitWithError(message)
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puts ###########################################
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puts message
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puts ###########################################
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exit(1)
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end
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if (ARGV.size != 2)
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exitWithError("We take two files as input, try again!")
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end
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# open the indexes
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index1 = File.new(ARGV[0])
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index2 = File.new(ARGV[1])
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# a helper function for comparing values
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def compValues(file1, file2, byteCount, type)
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index1Type = file1.sysread(byteCount)
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index2Type = file2.sysread(byteCount)
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if (index1Type != index2Type)
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print "#{type}, index1 (#{index1Type}) != index2 (#{index2Type})\n"
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else
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print "#{type}, index1 (#{index1Type}) == index2 (#{index2Type})\n"
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end
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end
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# a helper function for comparing values
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def compInts(file1, file2, byteCount, type)
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if (byteCount > 4)
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upack = "q"
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else
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upack = "i"
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end
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index1Type = file1.sysread(byteCount).unpack(upack)
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index2Type = file2.sysread(byteCount).unpack(upack)
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if (index1Type != index2Type)
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print "#{type}, index1 (#{index1Type}) != index2 (#{index2Type})\n"
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else
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print "#{type}, index1 (#{index1Type}) == index2 (#{index2Type})\n"
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end
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end
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# a helper function for reading strings
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def readString(index)
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buffer = []
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ch = index.sysread(1)
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while (ch != "\0")
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buffer.push(ch)
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ch = index.sysread(1)
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end
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buffer.to_s
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end
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# validate the magic number from both
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exitWithError("Magic number not valid for index 1") if index1.sysread(4) != "TIDX"
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exitWithError("Magic number not valid for index 2") if index2.sysread(4) != "TIDX"
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# validate the types
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compInts(index1,index2,4,"types")
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# validate the versions
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v1 = index1.sysread(4).unpack("i")
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v2 = index2.sysread(4).unpack("i")
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if (v1 != v2)
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print "version, index1 (#{v1}) != index2 (#{v2})\n"
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else
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print "version, index1 (#{v1}) == index2 (#{v2})\n"
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end
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# validate the filenames
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fl1 = readString(index1)
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fl2 = readString(index2)
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if (fl1 != fl2)
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print "filename, index1 (#{fl1}) != index2 (#{fl2})\n"
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else
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print "filename, index1 (#{fl1}) == index2 (#{fl2})\n"
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end
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# validate the sizes
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compInts(index1,index2,8,"sizes")
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# validate the T5?
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compValues(index1,index2,8,"T5")
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# validate the MD5 - just a byte, we don't write the MD5 sums in yet
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# validate the filenames
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fl1 = readString(index1)
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fl2 = readString(index2)
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if (fl1 != fl2)
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print "md5, index1 (#{fl1}) != index2 (#{fl2})\n"
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else
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print "md5, index1 (#{fl1}) == index2 (#{fl2})\n"
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end
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# validate the flags
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index1Flags = (index1.sysread(4)).unpack("L")
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index2Flags = (index2.sysread(4)).unpack("L")
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if (index1Flags != index2Flags)
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print "Flags are different, index1 = #{index1Flags[0]}, index2 = #{index2Flags[0]}\n"
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end
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def readSeqDictionary(file)
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puts "reading seq dict"
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sequences = []
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count = (file.sysread(4)).unpack("i")
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puts count
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count[0].times {|index|
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sequences.add(readString(file).to_s)
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file.sysread(4) # drop the sizes for now
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}
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sequences # return sequences
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end
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if (index1Flags[0] == 32768)
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puts readSeqDictionary(index1)
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elsif (index2Flags[0] == 32768)
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puts readSeqDictionary(index2)
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end
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# bump off the prop dictionary
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index1.sysread(4) if (v1[0] == 3)
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index2.sysread(4) if (v2[0] == 3)
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def readSeqEntry(i1)
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puts "--------------------------------------------"
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puts "Contig --> #{readString(i1).to_s}"
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print "bin width = #{(i1.sysread(4)).unpack("i")}\n"
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binCount = (i1.sysread(4)).unpack("i")[0]
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print "number of bins = #{binCount}\n"
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print "longest feature = #{(i1.sysread(4)).unpack("i")}\n"
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print "max bin size = #{(i1.sysread(4)).unpack("i")}\n"
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print "total bin size = #{(i1.sysread(4)).unpack("i")}\n"
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lastStartPos = -1
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binCount.times { |index|
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startPos = (i1.sysread(8)).unpack("q")[0]
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#if (startPos < lastStartPos)
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puts "bin at index #{index}, this start = #{startPos}, last start = #{lastStartPos}"
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#end
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lastStartPos = startPos
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}
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end
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def compContigLinear(i1, i2)
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seqC1 = (i1.sysread(4)).unpack("L")
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seqC2 = (i2.sysread(4)).unpack("L")
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print "seq count 1 = #{seqC1}, count 2 = #{seqC2}\n"
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puts "\nentries for index 1"
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seqC1[0].times { |index|
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readSeqEntry(i1)
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}
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puts "\nentries for index 2"
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seqC2[0].times { |index|
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readSeqEntry(i2)
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}
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end
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compContigLinear(index1,index2)
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print "Done!\n"
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# close the files
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index1.close()
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index2.close()
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