PK jf8 META-INF/PK if8+META-INF/MANIFEST.MFManifest-Version: 1.0 Ant-Version: Apache Ant 1.7.0 Created-By: 1.6.0_03-b05 (Sun Microsystems Inc.) Main-Class: seattlesnpstophase.SeattleSnpsToPhase Class-Path: X-COMMENT: Main-Class will be added automatically by build PK jf8seattlesnpstophase/PK jf8H H #seattlesnpstophase/AlleleFile.class1} HI H J K L MNO PQ RST PU VW X Y Z[ \ ] U ^_` abc d e fghdiscardedPositionsLjava/util/ArrayList;flagIbrLjava/io/BufferedReader;(Ljava/io/BufferedReader;)VCodeLineNumberTableLocalVariableTablethisLseattlesnpstophase/AlleleFile;findDiscardedSnps()VilineLjava/lang/String; Exceptionsi discardIndels&(Ljava/lang/String;)Ljava/lang/String;jdiscardTriallelicaddPositionToArrayList8(Ljava/lang/String;Ljava/lang/String;)Ljava/lang/String;delimtkLjava/util/StringTokenizer;getDiscardedPositions()Ljava/util/ArrayList;setDiscardedPositions(Ljava/util/ArrayList;)VgetFlag()IsetFlag(I)V SourceFileAlleleFile.java '/java/util/ArrayList !" #$ %&k lmADn op DEED6The + (inserted) allele for each site is listed below: qr 56Tri-allelic sites: 86 >?s tu vC wx yx: 9: java/util/StringTokenizer 'z {m |rseattlesnpstophase/AlleleFilejava/lang/Objectjava/lang/Exceptionjava/io/IOExceptionjava/io/BufferedReaderreadLine()Ljava/lang/String;java/lang/String startsWith(Ljava/lang/String;)Zequals(Ljava/lang/Object;)Zjava/util/Collectionssort(Ljava/util/List;)Vsizeget(I)Ljava/lang/Object;remove'(Ljava/lang/String;Ljava/lang/String;)V nextTokenadd! !"#$%& '()^**Y**+*+,-%&./)&*L+Z+  **` +  **` +  *+L++  *+L*L*=*d-**`*`W̱*J  !*"4$>%D'H(R)X+c/j1y2316+ l70$,-123456)v**L*L+ *+L++*9:;<!=%>(A+*,-*1237786)q)*L*L*L+*+L+*EFGHI'K+),-)123779:)t Y+,N*-W*L+*O PQR+* ,- 12 ;2 <=37>?)/**X+ ,-@A)>*+* \]+,-!"BC)/**`+ ,-DE)>** de+,-#$FGPK jf8d5^8 !seattlesnpstophase/Outfiles.class1 'R &S &T &U &V &W &X &Y &Z[\ R ]^ _ ` &ab cd &ef g h i jklmn jo pqrstu vwxbwAALjava/io/BufferedWriter; outfileAALjava/io/FileWriter;bwEU outfileEUfileNameLjava/lang/String;prettybaseFile#Lseattlesnpstophase/PrettybaseFile; sampleNames[Ljava/lang/String;K(Ljava/lang/String;Lseattlesnpstophase/PrettybaseFile;[Ljava/lang/String;)VCodeLineNumberTableLocalVariableTablethisLseattlesnpstophase/Outfiles; createOutfile()V Exceptionsy openOutfile writeSample(ILjava/io/BufferedWriter;III)ViIindbwbegin beginNameendsnwriteFastPhaseFile(Ljava/io/BufferedWriter;)V writeWarnings(Ljava/io/BufferedWriter;I)Vflag closeOutfile SourceFile Outfiles.java 4< ./ 01 23 ?< () @A ,) O<java/io/FileWriterjava/lang/StringBuilder z{_AA.inp |} 4~ *+java/io/BufferedWriter 4_EU.inp -+ z ~ < P S <fastPHASE -oSSGene__AA _EU  correct3 does not correspond to the AA and European samples <seattlesnpstophase/Outfilesjava/lang/Objectjava/io/IOExceptionappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;toString()Ljava/lang/String;(Ljava/lang/String;)V(Ljava/io/Writer;)V(I)Ljava/lang/StringBuilder;writenewLine!seattlesnpstophase/PrettybaseFilegetKeptPositions()I getGenotypes()[Ljava/lang/String;flushclose!&'()*+,)-+./0123456l**+*,*-7 8*9:./0123;<6a'*****0/* 7 !""#&$8 '9:=>?<6a* Y Y *  *Y** Y Y *  *Y*7'!(0*Q+`,8 a9:=>@A6, Y  ,, Y  *,,6*!, Y  ,6*,,66hH,*2,,*2,,*`2,,`67f/0182<3B4Q5i4o7s898;=>?@ABCDEF>H8f E*BCvBCNBC9:DCE)FCGCHCRIC=>JK6c+ Y  * ! *  ++ Y  * " *  ++7K+L/MZN^ObP8c9:cE)=>LM6I$+ Y * # +!+ Y * $ ++7STU&W@XDZH[8 I9:IE)INC=>O<6W**%**%7^_abc8 9:=>PQPK jf8W8 'seattlesnpstophase/PrettybaseFile.class1m DE F G H I J KLM N OP OQ R S T U V W XY Z[\]^ genotypes[Ljava/lang/String; keptPositionsIdiscardedPositionsLjava/util/ArrayList;brLjava/io/BufferedReader;0(Ljava/io/BufferedReader;Ljava/util/ArrayList;)VCodeLineNumberTableLocalVariableTablethis#Lseattlesnpstophase/PrettybaseFile;buildGenotypes()V lineArraylineLjava/lang/String;a Exceptions_ addPosition&(Ljava/lang/String;)Ljava/lang/String;i`concatPosition(ILjava/lang/String;)VallelediscardPositioninitializeGenotypesArray getGenotypes()[Ljava/lang/String; setGenotypes([Ljava/lang/String;)VgetKeptPositions()IsetKeptPositions(I)V SourceFilePrettybaseFile.java "*java/lang/String   !  9*a bc def g? hi jk 12 82 :; 56 >? @AN l2? !seattlesnpstophase/PrettybaseFilejava/lang/Objectjava/lang/Exceptionjava/io/IOExceptionjava/io/BufferedReaderreadLine()Ljava/lang/String;split'(Ljava/lang/String;)[Ljava/lang/String;java/util/ArrayListsizeget(I)Ljava/lang/Object;equals(Ljava/lang/Object;)Zconcat! ! "#$o**^**+*,% & '( !)*$c**L=+S+ N* 9-2*  *+L"*+L* d *+L%:  !"##7$@&F'S(Y/_1b2&*F+c'( W,-U./012$?=*++ N*-2*`-2*L`=**`+%"5 678$9,53;=<&*+13?'(?,-/456$}3, **2, S**2S%@ A!C2E& 3'(3337-82$f=**L`=+%H IHK& 3'(,-/49*$Z<**S%O POR&3'(:;$/*%U& '(<=$>*+% YZ&'(>?$/*%]& '(@A$>*% ab&'(BCPK jf8G$seattlesnpstophase/SampleNames.class16 #$ % &' #( ) * +,-./0 sampleName[Ljava/lang/String;()VCodeLineNumberTableLocalVariableTablethis Lseattlesnpstophase/SampleNames;createSampleNamesiIa getSampleName()[Ljava/lang/String; setSampleName([Ljava/lang/String;)V SourceFileSampleNames.java java/lang/String  java/lang/StringBuilderDY0 12 13 45DYE10E1seattlesnpstophase/SampleNamesjava/lang/Objectappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;(I)Ljava/lang/StringBuilder;toString()Ljava/lang/String;!@**/  T<= %*Y S =%*Y  S<=!%*Y  S!=/%*Y  S۱N #&,5NQWYb{ ~"#$"&>(/(\((/*)  >*+ -.!"PK jf8+seattlesnpstophase/SeattleSnpsToPhase.class1 <pqr s tuv p wxy sz {| } ~         # #  ' ' ' '  1p 1 1 1()VCodeLineNumberTableLocalVariableTablethis'Lseattlesnpstophase/SeattleSnpsToPhase;main([Ljava/lang/String;)V allelesFileLjava/io/FileReader;prettybaseFileaFileLseattlesnpstophase/AlleleFile;pbFile#Lseattlesnpstophase/PrettybaseFile;outfilesLseattlesnpstophase/Outfiles;fileNameLjava/lang/String;tkLjava/util/StringTokenizer;geneNamepreviousFoundGenebrAFLjava/io/BufferedReader;brPF sampleNames Lseattlesnpstophase/SampleNames;outfileLjava/io/FileWriter;bwBatLjava/io/BufferedWriter;outfile2 bwWarningiIerrorLjava/io/FileNotFoundException;error2Ljava/io/IOException;error3Ljava/lang/Exception;args[Ljava/lang/String; phaseFilesLjava/io/File;phaseFilesInDir[Ljava/io/File; SourceFileSeattleSnpsToPhase.java => java/io/File. = seattlesnpstophase/SampleNames >java/io/FileWriterlaunchFPhase.batjava/io/BufferedWriter = warnings.txt java/util/StringTokenizer =  alleles.txt java/io/FileReader =java/io/BufferedReader = prettybase.txt   seattlesnpstophase/AlleleFile = >!seattlesnpstophase/PrettybaseFile = >seattlesnpstophase/Outfiles = > > >java/io/FileNotFoundExceptionjava/lang/StringBuilderFile not found error: java/io/IOException IO error:java/lang/ExceptionError:%seattlesnpstophase/SeattleSnpsToPhasejava/lang/Object(Ljava/lang/String;)V listFiles()[Ljava/io/File;createSampleNames(Ljava/io/Writer;)VisFile()ZgetName()Ljava/lang/String;'(Ljava/lang/String;Ljava/lang/String;)V nextTokenjava/lang/Stringcontains(Ljava/lang/CharSequence;)Z(Ljava/io/File;)V(Ljava/io/Reader;)V startsWith(Ljava/lang/String;)ZendsWithjava/lang/SystemoutLjava/io/PrintStream;java/io/PrintStreamprintln(Ljava/io/BufferedReader;)VfindDiscardedSnpsgetDiscardedPositions()Ljava/util/ArrayList;0(Ljava/io/BufferedReader;Ljava/util/ArrayList;)VbuildGenotypes getSampleName()[Ljava/lang/String;K(Ljava/lang/String;Lseattlesnpstophase/PrettybaseFile;[Ljava/lang/String;)V createOutfilewriteFastPhaseFile(Ljava/io/BufferedWriter;)VgetFlag()I writeWarnings(Ljava/io/BufferedWriter;I)Vflushcloseappend-(Ljava/lang/String;)Ljava/lang/StringBuilder;-(Ljava/lang/Object;)Ljava/lang/StringBuilder;toString!;<=>?3*@ A BC DE?pYL+MN::Y: Y : Y: Y : Y : 6  ,, 2, 2: Y :  : NY, 2:Y: -z p-Y, 2:Y: Y!:"#Y$%:&'Y-():*+ ,- *. ./ /WN1Y234-56:N1Y284-56N1Y2:4-56BE0Bb7B9@/# $'()+!,&.1/<1G2R5\6f7o8|9:;<=?@BCEFHIKLMN(5.R3S8T=UB\EVFW_\bXcY|\Z[]A FGYHGCIJ.KLMNoOP |QR SP0TP-UV*WV!!XY1Z[<\]G^[ R_] U`a Fbccdefghi jklmnoPK jf8 AMETA-INF/PK if8++META-INF/MANIFEST.MFPK jf8ADseattlesnpstophase/PK jf8H H #useattlesnpstophase/AlleleFile.classPK jf8d5^8 ! seattlesnpstophase/Outfiles.classPK jf8W8 ' seattlesnpstophase/PrettybaseFile.classPK jf8G$"seattlesnpstophase/SampleNames.classPK jf8+!'seattlesnpstophase/SeattleSnpsToPhase.classPK^86