PK pr> META-INF/PK pr>META-INF/MANIFEST.MFManifest-Version: 1.0 Ant-Version: Apache Ant 1.7.1 Created-By: 11.0-b16 (Sun Microsystems Inc.) Main-Class: vcf2bco.Main Class-Path: X-COMMENT: Main-Class will be added automatically by build PK pr>vcf2bco/PK pr>IE++vcf2bco/FormatVcf2bco.class1c p o o o o # # # ! ! ! , " 0 / /    # : :  :  : o  :       " / " " # ^ ] ] ]!"#$ ] ]%&' #( )* +,-. chromosomes[Ljava/lang/String;vcfFLjava/io/File; outputStemLjava/lang/String;#(Ljava/io/File;Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethisLvcf2bco/FormatVcf2bco;go()ViIc genoflagstLjava/util/StringTokenizer; genoflags thisinfcolgenostgenosttLjava/lang/Throwable;NJsiteinfogenocolstrconsensusquality strsnpquality strRMSquality strreaddepthinfosticscore isnpquality irmsquality ireaddepthcscoreB snpquality rmsquality readdepthcols genocolflagintchrstbrLjava/io/BufferedReader;bwLjava/io/BufferedWriter;strout[Ljava/io/BufferedOutputStream; outputFiles[Ljava/io/File; currentSite[Jpreline afterlinemaxrd maxcscore maxsnpqualitymaxrms genoqualidxgenoqualityidxdefinedZcountsumFileterrFlag StrChrToInt(Ljava/lang/String;)IstrChrbytechr SourceFileFormatVcf2bco.java wjava/lang/StringMT12345678910111213141516171819202122XY qr st uv ~ java/io/Filejava/io/BufferedOutputStreamjava/lang/StringBuilder /0_..bco 12 w3 45 65java/io/FileOutputStream w7 w8java/io/BufferedReaderjava/io/FileReader w9 :2 ;2 <=# >? Line: /@java/util/StringTokenizer ABC D-* Format error. Column number must be >= 10. E F3 G2GQ H: wI J KL0; M5DP= NOMQ=P QRS TUjava/lang/Throwablestrconsensusquality =strsnpquality =strRMSquality =strreaddepth =-Exception. Exit. Quality score format error: VW XY Z [Maximum read depth = /\ _.bco.txtjava/io/BufferedWriterjava/io/FileWriter w] X3 ^Maximum SNP quality = Maximum consensus score = Maximum RMS score =  Exception! Internal code: /_ `2Ma bvcf2bco/FormatVcf2bcojava/lang/Objectappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/String;)Vexists()Zdelete(Ljava/io/File;)V(Ljava/io/OutputStream;)V(Ljava/io/Reader;)VreadLinetrimequals(Ljava/lang/Object;)Z startsWith(Ljava/lang/String;)Z(J)Ljava/lang/StringBuilder; countTokens()Ijava/lang/SystemLjava/io/PrintStream;java/io/PrintStreamprintln nextTokenindexOf'(Ljava/lang/String;Ljava/lang/String;)Vjava/lang/Long parseLong(Ljava/lang/String;)J hasMoreTokens substring(I)Ljava/lang/String;java/lang/Double parseDouble(Ljava/lang/String;)Djava/lang/Mathround(D)Jmax(II)Iwrite(I)Vcloseflush(I)Ljava/lang/StringBuilder;(Ljava/io/Writer;)VnewLine-(Ljava/lang/Object;)Ljava/lang/StringBuilder; toUpperCasejava/lang/IntegerparseInt!opqrstuvwxy**YSYSYSYSYSYSY SY SY SY  SY  SY SY SY SYSYSYSYSYSYSYSYSYSYSYS*+*,*z{ |}stuv~y * L*!:*":* : 6  *l !Y#Y$*%&%* 2%'%()S 2*  2+W "Y,Y 2-.S  P  :  : 6 6 6666/Y0Y*12M 7,3Y: a74: 567ػ#Y$%8%9(L:Y;: : :< =>?6 @S2:lABa:YCD::@S@S@S2A562A562A5662E62F72: 2:2:G:G:G::YHD:I1@:  J7  K: L7  K:AB8:YCD: :!! @S! @S! @S!2:6 6!6"6#MN6 MN6!MN6"MN6#:$=#Y$P%%(?=#Y$Q%%(?=#Y$R%%(?=#Y$S%%(?=#Y$T%+%(? #U6   U6 !U6"U6 6 !6!"6"#6# d6$!d6%"d6&#d6' / / /7((=2V2V2V2V \/ aP( a7(2$V2%V2&V2'V \/ aP42$V2%V2&V2'V \/ aP: D,W6*2X2Y=#Y$Z% [(?!Y#Y$*%\%():]Y^Y_`N-#Y$Z% [(a-b-#Y$c%[(a-b-#Y$d% [(a-b-#Y$e%[(a-b-f-g>M=h?=#Y$i%+%(?=#Y$j%,k(?O3qO4=qO>nqOz>$. /0 1-2^3i4r671:;=>?@CDFGHIJKL MNO!Q+R3S4W>XHWN[U\e]r^x_`abcdeklnqrstuvy z{|"}*4<?JW]fox $=>GPYbo|#-7AMWaku~*.FJ b f j nqrz{1#s 7rQxKr$v W( ]"r!$B(vvvvvv u !"#$%&'er!avo xvW a N v v   tr:|}v yH<*lK*5Y<*5Y<*m5 *5Y<*n<M<:?BOz.  !$#6$:'?)F*{ CHvEPK pr>P CCvcf2bco/Main.class1S * +,- ./0 +12 3 456 789: *; < = >? @A([Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablepileupfLjava/io/File;outstemLjava/lang/String;tLjava/lang/Throwable;thisLvcf2bco/Main;args[Ljava/lang/String;main SourceFile Main.java BC DE.Parameter should be: [vcf file] [output stem] F GHExit IJ java/io/File H KLPileup file does not exist. vcf2bco/FormatVcf2bco Mjava/lang/ThrowableParameter error.java/lang/StringBuilder NO NP QR vcf2bco/Main java/lang/Object()Vjava/lang/SystemoutLjava/io/PrintStream;java/io/PrintStreamprintln(Ljava/lang/String;)Vexit(I)Vexists()Z#(Ljava/io/File;Ljava/lang/String;)Vappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;-(Ljava/lang/Object;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;!|*+ +Y+2M+2N,   Y,- W%MY,VY F"-18@HL V&Y#Z$b%{(4-)1% Z!!"|#$|%& '8 Y*W . /  %&()PK pr> AMETA-INF/PK pr>+META-INF/MANIFEST.MFPK pr>A'vcf2bco/PK pr>IE++Mvcf2bco/FormatVcf2bco.classPK pr>P CCvcf2bco/Main.classPK<$