# HG changeset patch # User peterjc # Date 1393865361 18000 # Node ID 5bbaa930d7fa66f24de97dc93f1544af766c10ff # Parent 4c6e4d583b8f903fe8b2f6da94c51ceb4e234d85 Uploaded v0.0.2 preview 9, more functional tests diff -r 4c6e4d583b8f -r 5bbaa930d7fa test-data/U13small_m.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/U13small_m.fastq Mon Mar 03 11:49:21 2014 -0500 @@ -0,0 +1,104 @@ +@122533a.t3 +ACGCGTTATTAAAGACTTTTTTTTTGGTTTTTTTCAAGTTCAAGTATTCTTTATTCAAAGTTGAAACATGTACCATACTGCATTATTGCAAAAATTCACTGGTACAAAACACTTTGCAGCTGGTGAGAAGGCAATAAAAAGTTGATTTTTAAACTCATTACTATAAATTATTCTTACAGTACTTTGCAAATTCAGAATTTCAAACTGCATGTTCTTTTTCTAAATTGCCCACAGTACTCGAGGTTCCTGAAGCTAAGGCAGCTGTTTCATAGGAGGGGGAAGAAGTATCAAATCTCTTGGGATTTCCATTTCTCTTTCCATGCCGACATACTTCAGGGCATCTTCCTGACTGTCTCTTTTTTCGGGAAACTTCTCTTCGCCAATCTGGATGGCTCTCTCGGCAAAAATACCTATCCTGTGATCACCGTTAACCATCATAACTTTTGCATACCACTTTGGATTTACCACCGATATGCCACAACGATTTTTGTTACCCTTGCAGGTTGCACCACCCAAAATCGTTGTTCTTTTGCCCTTGCCAAATTCTGGGCCCCAAGGGCCAATTCCCCAAAATTAATCCTTTTAATTTCGTGGGCCGCGTTCCAGCTGTCCCCCTTGTTGAAGGTTTTTTTTCGCCCCCCGGCTCTCCCCCCCCCTTTTTAAACCCCGTAAACCATTATAGTTGGTTAAACCCCCGGGGGGTTCCCCCTTGTAAATTTTACCCCCCCCTCTCCCCCATTTAAAAATATGTGCCCTTTTTCTCCCCCCCACTGGGCCCGGGGTTTTCTCCTATTCCGGGGAAAGAAAAACCCTGTTTTCTCTTCGCCAAAATACTCCCCCCCCCCTTTTTATAAAAAAAAAAAAAACTTGGGGGCCCCCACCCCCCCCCGGGGGGGAAAAAAAAAAGCGCGGGGTTTTTGCGCGTTTTTTTTGGGGGGGGGGGGGTTTCTTTTCCCCCCCTTTTTTCCTTCCCCCCCAAAGGAGAAAAAATCTTTTTTGTTGGGGCGCCTCCCGGCGCCCCTCCCGGGGTTGGCGCGGCGAAAACGCGGTTTTTCCCCCCCCCCCAAAGGGGGGGGCGCAGATACCGCGTTTACTCCCCATAAATACTCCGGGGGGGAATAACATCCCGGGAAAAAAAAATTTTATATCTATATATGGGGCCTCCCAAAAAGGGGCATAAAACACGGAGAAACCGGCGCCCTTGTGTGGGCGTTTTTCTCTCAATGGGCGCCCCCCCCCTCAACAAAAATAAAAA ++ +'%+2*(6.+;8:2)+(*).1AA88(-,(88AA=;==99@;BC21-,,-8?91695?=5:7?;11,)(*-55==@:BABBAEABABA?BA??;>;@;;7*0/*22;@BCCBE@F?@??8??678>0,6?9@>8>;?CAEAD??>@DEA>?4>A?C?8;7:A?ACCAADB>=-5;3>:/6-3:6@A4597->58:6318=B?DAA?72*/+.1)01771-.1.+/+).(610)-7-(,0-8968?:/A/4928,))-+1))21/1-6??>9:3-572629.)2510-+,,/5,3,*+.)*.)*+/.7>-..00,+.40:82+68.;2/,-.)+.-+*)**)626;?988623-37./5/1))78@>G;5:>7:/--68;8?A40/,.1--.5:768.4))(())(+%)))+*))**((+(*(*0*--/;::2,+()))++)**,--:2**2/2(*)+,*))+((0-,/*))*+)*+-2+()++/**,,*-=751,,)((*25;(,,2),(-.(*,-+1-.,,./-%.%*1,,'()+)+('%.*)*))0,&(+(),),+++,/*./*,*,))))*)(%%%+-%**,3.+)0**202%-0,,20*/(*,*++))(0())()'(+))17:84.)+1.)))+))41,)$'''))'*0))&),3-,))++-)*+..*',,),+.+.((.**+++),*+,)%(.,/51+()''),.,*/--+(002/((,&+&*,*,+,,,*)*),*)-))*+*%.***,(+))$'&+%)*-'%*0.*+***///+.,,*)*),-*267<;30-(%)**(,1456;63)*,*,+=759.3-.342-*-+0())'))**,)200,)025))++++(*/466,',$))12*&///,)()*)/)+-),2-,**,*1.1.,***,)/,22-*%)),*&/)+',,++)/,**)((()))*,%(*)+)))(*&)).03&1;5:22))+))'.-))+&+/+)))((+*+,33=36-,,3//,+)+)),./+,)*+))*(*)))))%)),)$'+)+,*&)+++,-))**++7702&**1+)-*(*-+)+*)))/1.0.+,-)*)(**.*)**')'')$*.-)42)**00),+*)))%*,)).+.-.****(()(+)-)(()*.())((-*,(++//+,1*.-()/31/8/,/47;7,+(),324)*))(**0C@ +@122533a.t7 +GTTCGAGCAATATCCCTACGATCAACTAGAACAATGATTTTGTGGTGGATGCAACCCGCAAGGGTAACAAAATTCGTTTTGCAAATCATTCGGTAAATCCAAACTGCTATGCAAAAGTTATGATGGTTAACGGTGATCACAGGATAGGTATTTTTGCCAAGAGAGCCATCCAGACTGGCGAAGAGCTGTTTTTTGATTACAGATACAGCCAGGCTGATGCCCTGAAGTATGTCGGCATCGAAAGAGAAATGGAAATCCCTTGACATCTGCTACCTCCTCCCCCTCCTCTGAAACAGCTGCCTTAGCTTCAGGAACCTCGAGTACTGTGGGCAATTTAAAAAAAGAACATGCAGTTTGAAATTCTGAATTTGCAAAGTACTGTAAGAATAATTTATAGTAATGAGTTAAAAATCAACTTTTATTGCCTTCCACCACTGCAAGTGTTTGTACCGTGAATTTTGCAATAATGCCATATGGTACATTTTCCACTTTGAATAAAGAATACTTGAGCTTGAAAAAAAAAAAAAAAAAAGATTCTTTATTTAAGCGGCCGCGAGCTTTTCCCTTTAATAGGGTTAATTTAACTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX ++ +&&&,1/?/,/(+)+'('+)(1.+*+,0**1-1574=====EBAABA=:=56;6879=>7-025>>;?ACBA?A?AAAEBEA?ABAA=FF@@??AA?@AA?A=@=A<@==@=@E=@@A@=A@;2:22-&623@DFBAABB=59;/888B?B?<72;;:@==84.)1,9AAEEFECB???;B?<>??;BCBAAAAAA?==>=@DA??;7.<8<524/37AA??><.,1.87====AEB@AAA===869BA@?=@=?AAAABBABBABAAAAAC==A??ABBBEEDAEEBA97:053064:A7;)2,,2.63:5==>=@:::A@;A=7A==A?AAA?A=9====??=D====B@@=:E=A@AAA?;4:6=64==?AABAB05**33/,116>E@==9=:=:?@=:A=466,-)*..--/1230627:3666;.,*(1,996E<6;5@=8=@8-(/))..033AAA:992/2/>674;65936400,-.62++,$**-8;34.**)118''4.**)+)))).11,**..-(.()+*))+$)$+')12,02*,.-,+*(,6*)*)1)(..8'!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@122533b.t3 +ACGCGTTATTAAAGATTTTTTTTTTGGTTTTTTTCAAGTTCAAGTATTCTTTATTCAAAGTTGAAAAATGTACCATACTGCATTATTGCAAAAATTCACTGGTACAAAACACTTTGCAGCTGGTGAGAAGGCAATAAAAAGTTGATTTTTAAACTCATTACTATAAATTATTCTTACAGTACTTTGCGTATTCAGAATTTCAAACTGCATGTTCTTTTTCTAAATTGCCCACAGTACTCGAGGTTCCTGAACCTAAGGCAGCTGTTTCAGAGGAGGGGGAGAAAGTATCAAATCTCTAGGGATTTCCATTTCTCTTTCCACGCCGAAATACTTCACGGCATCTTCCTGACTGTCTCTTTATTCGGGCAACATCTCTTCACCACTCTGGATGGCTCTCTCGGCATAAATACCTTTCCGGTGATCTCCGTTAAACTTCTTAATTTTTTGGCATCCCCGTTTGGGATGTACCGCACTGAATTGCAAAAACTAATTTTTGTTTACCCCTTGACGGGTTGCCATCCCACCCCAAAAATCCTTTGTTTCAAATTTGCCTCCGTGACCAAAATAACCTTGGGCCCCCCTAATGGGCCAAATTTCCCCTCATTAGTTTGAATTTCCTTTTTAAATTTTCCCTTGGTCCGCGTTTCCTAAACTCCCTCCCCCCGGTGTTGAGGGTTTGGTTTTTCCCGCCTCGGCAAATTCCCCCCCCTCACTTTTTAAAAACCCCTGTAAACCCACTTGGGTTTTTAAACCCCCTGGGGGGTGTCCCAAAATTTAAAGTTTAACCCAATCCCCACACATTAACTTCCCTTTTCCCCCCCCCTGGCCCGTTTTCTCCTTTCGGGAGAAACCCGTTCTGTTCCCCCCCTCCCTTAAAAAAAATTCCCCCCACCCCCCAGGGAAAAAGCGGTTATATCCTCCTTGGGGCCTCTCCCCCTCTCCCCCCCCCGAGTATATCTTTGGTGTCCCCGGCGCCTTTTTGCCCGGAAAATGTGTTATGCCCCTATAAAGGGGGGTCTATGGGGTTTCCCCCACACCCGGGTTCCCCCGTAATAAACCTTTTTCTCCCCGGCCCCCAGGGCGGAAGCCCCAAGGGGGGTTTCTCATGTTTTTTCATGGGCCCCCCCCCAAAAAATAAAAATTAG ++ +&%,0*)2*)209.+)'.+=A?@68),,(<CD7456<:?A3.31/8=05.51880+*+-31====AAAAAA???B@>@A;9:9;@;@@????::?D9:520/52:A??;>>AA@BECC@>@C@BAACDAA@@@@:>97??A@BBC?=13*(*-3,7764.,.6<,.?;?22)2/4?ACAA?@@@@@:;9-;;<<*'981=53./2))*3,,.)(()*,+.2.0218.)05%3'))(**/31/**(+/)28.,.)6&,,++)*+(/+0*)*2-0)(&,0,,/25*,*30/*,*.5C;;,),*)+**,(%*)0,*.))''*+4)/*),,.-+)*+*+5:=8*.+,3.1.)*.*),,-1)(+**(.**-**(*(,*)**+-1,%%(****)((+(+..*+*(..,--*+(/%)*++*88231.,,*/+,,*+**,,))))..))509-,21:@50))*$(*&-,(,,,(**)(*+.**'***005711%%*(%+*$+))/+4.2)((+*)))))),35()())))*0()+*-)-)*,+,.*.1,++)()*&)7/.+*..9;)(('))**/4/1%+369160)*+*+.2&,**(*&**)+**,*,*2**021&*263+*+*()+***.-'))))))*+++,*;6+)**)+))+'()*/,-)*)*,-6.,*(-,;A77+++,,***+11030,,*((())((..+***+))*)*)***6:79-+)))),*)*-.510,.)*,+/0,,,,31,,*)+*,8:60+0(****1*(&)*.((+(*+*)+-+,).++/+,&*,3:99..,+++**)*-+)(&)*,*1*+*))))'-+)/+**&)()%,-,133**)(*(+%%.)**,)%+*(***0++()()+()+).+))*+)**)))))57*-))/51(*)**,*)))(*/2,++*-1('**/+.-***,*))),))**),%,),5*+,*-/+)()))*7:5+(*(*+*+278DA851)))()*,.,++**)))) 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+CCGAGCAATATCCCCACGATCACTAGAAAATGATTTTGTGGTGGATGCAACCCGCAAGGGTAACAAAATTCGTTTTGCAAATCATTCGGTAAATCCAAACTGCTATGCAAAAGTTATGATGGTTAACGGTGATCACAGGATATGTATTTTTGCCAAGAGAGCCATCCAGACTGGCGAAGAGCTGTTTTTTGATTACAGATACAGCCAGGCTGATGCCCTGAAGTATGTCGGCATCGAAAGAGAAATGGAAATCCCTTGACATCTGCTACCTCCTCCCCCTCCTCTGAAACAGCTGCCTTAGCTTCAGGAACCTCGAGTACTGTGGGCAATTTAAAAAAAGAACATGCAGTTTGAAATTCTGAATTTGCAAAGTACTGTAAGAATAATTTATAGTAATGAGTTTAAAAATCAACTTTTTATTGCCTTCTCACCAGCTGCAAAGTGTTTTGTACCAGTGAATTTTTGCAATAATGCAGTATGGTACATTTTCAACTTTGAGATAAAGAATACTTGAGCTTGAAAACAAAAATGTATCTTTATTAAAGCGGCGCAACCTATATCCCTTTTAAGTGAGGGGTTAATTTTAACTTTGGGCCCTGGCCCTCCTTTTTTACCAACCTTCTTTGAACTGGGGAAAAACACCTGGGCTTTTACCCAACCTTTATATCCGCCTTTGGGCAAACAAAATTCCCCCTTTTTTCCGCCAAAGCGGGGGGTTTTTTTTTTACCCAAAAAAAAAGGGCCCGCCCACCCCCTATATTTGCCGCCCCTCTCCTCCCCAAAACAATTTTTCCGCCCCCCCCCCCTTTAAAATTTTTGGGCGCCAAAAAATGTGGGGGGGAAACCCCCCCCCCCCCCTTTTTTTTCCCCCGGCGCGCCCCATATTTTTAAAAACCCCCCCCCCCCGGGGGGTGGTTTTTTTTGTTGGGGGTTTTCCCCCCCCCCCCCCCCCCCACCCTTTTTTTTAAAAACCCCCCTCTATTTTAAAACATCTTTTTGTTGGCCCAAAGACCCCCCCCCCCCCTATTAATAAACCCCCCCCCCCCCCCCCCCCCTTTTTTTGCCCCCTTTTTTCTCCTCTCTCCCCCCCCCCCTTCCCCCCCCTTTTTTCCCCCCCCCCCCCCCCCCATTTTTTTTTTTTTTTTTCCCCGCCCGGGGTGTTTTTCTCCCCCCCCCCCCCTTTTTTAAAAAAAAAACCCTCTCTCTAAAAAAAAAAATTGCGGGGGGGGGGGGGGGCCCCCCCCCCCTTTAGGGGGGGGTTTCTCCCAAAAAATTTTTATTTTTTTCTTTTTTAGGGGGGGCCCTCCCCCCCCCCCCCCCCCCCAAAAAAAAAAATTTTTTTGTTTTTTGGGGGGGG ++ +'$(-,-4-)'()**'/4+7*+**,()8)(4/16458AAEAD?368/1:14489>5*-13;@::8D>>>>8>BABB@AAAF?AAA?=@BBA=??A@AAAAAAAABA=@=:=D>?AAAA@=@@=BF@=8<6+,(../@ACBBEAA>44718:ADA@;;99:7:DBC650)2+7AAAFFAA????<;?==;<<5<=AA?A<<..3,78@==B===@AAAAA@???@AA??A?ABAEEAABBBA?A?A=@@<;9@?ABFBFEBBAAAB>;9453054;B?A05..87=A?=AABAA9:A?A;E6<<9>==AAABAAAA???CAA?=====??=>@=<<8;?=A9:3;;7EAABABAEAAA566:69A==@@EAA=@==@EDCAAAA>====?====:=AAAA==B@===>=@@9:=541.52371=E@4;;9;4@>@>=@?=55666)*,(),--/@;?@120,*)-**./:11(*(++')'.+)'&&&&&'''+)*)+')01-04**(,-2,,**-,.*./52./62722--++,)-(*.2+()+---3//1**2986.0-3-+.-*''()-',.((%(,%*,))))))))*42/05<-24*%+(..*+0+**.62,011+))*+,+-,)*+.-,,())),+)('))*,**))1201.)/52.**+'.-*)))')).40***562/,,,)000,07:DBC0/,,+,))+&-),())).)*+++)+'(&.&.-0>66,*-)1++'-+)*(*+14.,))*(*.),-1772***%*.2,,*&&&%,(()()(,+-**)()*,,7463)*&)*+-.:17DD3+)))))))))*(**'()&&))&&*)(%)()1/*./-'*%(,+2.)&...+)))'+*'&&)))()*1,-)(+(+**,.+))&&'+)*))2.-.2*.**-('))&))**2+,*)&+((()))-))%))&))))))))))$$--0)))')'&)***&)+((((-114*2-+*))$)),(),(&**086><6.-*,)+65=D76),*16/)))+*'*(+*59/.())**.++$--1DE5/-,-)+)(*,,0+,.3)+*+)&&**+**-,-/*./+((()%&++988A8A774.*(&'(+()))-)*0,%(***-.*2-0294*())))')(')41+/****&))'+'++,*)&(+,,=/-)(()+-()),2A@ED5;=@;AAABA636166?A34566;:57B??;;>>??9=.0.*.17:=@=@?;;818;??@A?CDDAACF@>=9??ACA@@@@;?73/88.07C9;/2618?ADAC@@AADA>7>+8;7A<7:4?C@@B@CDDA98*.34A643057698-+24,/*-.),*)((()'+933((1*0,),1191)()212//---*(/)%(),*+.0.222.-211****----*%,&..//-**%*)%4:05993-;7<23)(*11,)))++))*(,/*,.,10.2.()1*(*/)***,.42*-)(3*-<,*,-,*52,*4.-/,(-**)*0))'+$)/,.;:0-4+,-*,,*0421/-,+5,(*)%..+0*+/(),5/33*)(+*(()),)**(+,,5:9*(**)**-,*))*(.*,.**)))**,,**9>7+**)**+.*)'')%(),)++.-*+()(,**)*,+,3.-3//464=4-79)/5;.*)***(++.((/,,3..559/+)(*,*++*,))(-**)**+,)))(-))*/-*,,*,)*+),--2+***,*+)&2731-7/,-*)*-*-/*))**(**-,-9-01*,-+**)/53*-,-***.-))*(+**+,)++++)()*01*0+*-1.-+*))*+*+,)*.0**,(%**)))+--)*.&*++,(()())27+*++*(*,*+++**+,;4/*-53,0()((*+6++*(())(+)(,')-)))(*)(/,,)))++*+*0+*1156-*(((.-****+1)**+**))'+))**+*-,)()-47776;30.),00,+))0*()(*)+++,+(*+*))++*)%*(&%1**,/1,**).**),*)),**+))**13,+)))),***)%*.1:8;;)*..5551-/-,.,-,+)*-33-*)))),**-),10*())*))))*0+*)-001/*,)*+,+20>;::950526/)**-))*+*()*,,, 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+GTCTCTTTTTTAGAAATTTTTTTTTCAAGTTCCAGTATTCTTTATTCAAAGTTGAAAAATGTACCATACTGCATTATTGCAAAAATTCACTGGTACAAAACACTTTGCAGCTGGTGAGAAGGCAATAAAAAGTTGATTTTTAAACTCATTACTATAAATTATTCTTACAGTACTTTGCAAATTCAGAATTTCAAACTGCATGTTCTTTTTCTAAATTGCCCACAGTACTCGAGGTTCCTGAAGCTAAGGCACCTGTTTCAAAGGAGGGGGAGGAGGTACCAAATTTCAAGGGATTTCCATTTCTTTTTCGATGCCGACATACTTCAGGGCATCAGCCTGGCTGTATCTGTAATCAAAAAACAGCTCTTCGCCAGTCTGGATGGCTCTCTTGGCAAAAATACCTATCCTGTGATCACCGTCAACCATCATAACTTTTGCATAGCATTTGGATTTTCCGAATTATTTGCTAAACGAATTTTTTACCCCTGGCGGTTTGCATCCACCACCAAAATCATTGTTTCATTTTGAACAGAAAACCGCACATTTTTTTTTTCATTACAACCCCCTTCCCAAATTCTGGGCCCCAAAGGGCAAAATCCCCAAAAATTGAATTCCTTTTTAAATTTCCCTAACCCCTTTTCTAAACTTGTTTCCCTTTTTTTAAAAATTGTTTATCCCCCCCCTCATTTCCTCCCCCACCCTTTTGAAAACCCGGAAAACCTTAAATTTTTTTAAACCCCTGGGGGTTCCCCCAAAAATTGTTAACCCCACCCCTCCCCTTAAAATTGCGCTTGTGTGCGCCCCCCACATGCCCCCCCTTTTCTTAATCGGGAAAGAACCTTTTTTTTCACCACTCTTCCTTTTATAATAAAAAAAATCCGCCCCACCCCCCCCCGGGAAAAAAAAAGGGGGTTTTCTTTTTTTGGGGGGCGCCTCTTCCCCTTTTCTCCTCCCTCCACAAAAAATCTCCTGTGTGCCCCTCGGGTGTCTTTTCGGGGGTGGGGGAAAAAAAAGGTGTTTCTCTCCTCCCCCCCCCCACAAGAGGGGGGGGGGTAAAAATAGGGGTTTTTCCCCCAAAAAATATCTGGGGGGGAGTAATAAAACCCCCCGGGAAAAAAAAAAAAATTTTTTTTTTCATCAAAAGAGGGCGCCGCTCCACAACAAGGGGGCGCAAAAAAAAAACTCTTATAAAAAGGGCGGCGCCT ++ +$&&+&)&))+)('+'$&.3AAAA??==736).*()1244=A@8;.&028=@A6:@;?==;>=:5==?AA?A?@A@DGAACC????:;@<<8;788*/*461@96/725;>9<=,+-&+*,B=>A97<)1.*7640/),/*./,)2--16,41/6.315:8>D@AAA;9/()533*/39==;:12866<775886?C;;8A8;13-192;,6;9?C>4;=@B@@E8553????7:059/+/-,,,.02638:6931342::==811,.,2,5/,-2)*/1**0,,)*.*,**)*55494=>?65*31%**,017535/-%*/.5/*,,*2,*,%+++2&-)*+1)+50746.**2,,/*+2***2/-*5*)*+05201,))1+))%()$.2.)0.1-%12;00-*,*7**028<6:8,2-()())))(**+0/6/66>B52..-*55;71.-*)0/,-*+5++*1**'*,51**)+&++***,.=503-,*(3+)25).5/,)++,'%))))(+)++2,,+((),,0+)))))(((,)()))).1/./0*-/,4**,,0/6+,())),.,)$**+/37-1,.))(+)')/+*..00+)(.-).22*%0642**.+33+**)),+)**/(**,*))),+)+*-,+()+(*+1+))))(,-++$(-++)+.1*)))(&*)++,+*+032*-(%)&*(*,,,)+$))))*..6/.+))$+)%(&/&*),+.+),,)))'(,*(**)(++*2*+).)),9@A1,)****,****+))&)')%+-/20,034/+)-1-/++,--)20-1)**)(1--+-(')+*+$)),)+240,,-+-+*+))1)*))*,*).+,+*-+,200--5))++))694-10760-)++)*-0-*+)(-+(**--/*)**))')))+0))**+'+**)'''&*-,*+*&)**+-//1-*++/+*,***-+-,202+))./1**2),+,39;52,,*+)))+)/65*))''))7797-**(*()**-,--//2/***..*79,&*&(($)--+.,*,*---30C*))()))+(*)+)(&)*())))***2 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b.t1 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++ 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+@230375b.t2 +GAAACTAGAGTCCTGTACTTAGCTAAACCTCCCCCTCCTCTGAACAGCTGCCTTAGCGGCAGGAACCTCGAGTACTGTGGGCAATTTAGAAAAAGAACATGCAGTTTGAAATTCTGAATTTGCAAAGTACTGTAAGAATAATTTATAGTAATGAGTTTAAAAATCAACTTTTTATTGCCTTCTCACCAGCTGCAAAGTGTTTTGTACCAGTGAATTTTTGCAATAATGCAGTATGGTACATTTTTCAACTTTGAATAAAGAATACTTGAACTTGAAAAACATTAAAAACAAAAAAAAGATCTTTATTTAAGCGGCCGCAAGCTTATTCCCTTTAGTGAGGGTTAATTTTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX ++ ++)))&()*,)&)))')*))))+/,*,,-12A?<77>A@A<7/.&**)066A9?89,2-*11263-133:*30155DC=BE@?@??@@@9@==@<865:9=DD@@D;;?===?;@99;7;;?DA@@@>????A?BA:<:;??AAAC@A=B=;??DA?CEF@AAD@CA@ACAADBEA@????ABBAA@@AACABF@>DDA@@=????>7;2*658==?==?ADC8>82?86?D@>@@?>??>???@;:9:=::=9:3<57AC===??A;3,/)%%)*&*-),''//..714,))(-1,7773-/;/**.5---2=8???<999=A?A<46525-1697?<<>==A>!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@230375b.t3 +CCGCGTTAATAAAGGCCTTTTTTAGGATTTTTTTTTTCAAGTTCCAGTATTACCTATGCAAAATTGAAAAATGTACCATACTGCATTATTGCAAAAATTCACTGGTACAAAACACTTTGCAGCTGGTGAGAAGGCAATAAAAAGTTGATTTTTAAACTCATTACTATAAATTATTCTTACAGTACTTTGCAAATTCAGAATTTCAAACTGCATGTTCTTTTTCTAAATTGCCCACAGTACTCGAGGTTCCTGAAACTAAGGCAGCTGTTTCACATGAAGGGGAAGAATGTACCAAATTTCATGGAATCCATTTCCCCTTCCAATGCCAAATAACTCCGAGGGCTCCACCCTGCCTTTTCTCTGTATCCAAAAAACCCCTCTCGCCCCCTCTCGGAATGGGCTCTCGTGGAAAAAAAACCATCCTCCTGTAATATCCCCGGTAAACCCATTAAAAATTTTCGGCAAAAACTTTGGTGGGATTTCCACGAAATATTTTGCAACAACCAATTTTTTGTCCCCCCCGGCGTGGTCTGCCCCCCACCCAAAACATCCCTTGCTCCTTGTTAAAAAAAAAACGCCCCCCCTTTTTTTTTTCCAACCCCCCCTCCCCTGCCCAAAATCCTGGGCCTCCGGAGAGGGCGCAAAACTCCCCCAAAGAGATAATAGATTCTTTTTAAATTTCCGTAAATCCCTTTTTCACACCTGTGTCTCCCTCGTTTTAAAAAGGGTTTACCCCCCCCACAATTTCTCCCCCCCTCCCTTTCTAAAAACCGGAAAACCCTATAATTTTTTAAACCCCGGGGGGGTGTCCCCAAAGTAGATTTTAACACTCACACCCCCCATTTAAATTGTGCCTTTGCCCCACACTGGGCCCGCCTCTTTCCAATTCGGGAAAAAACCTTTCTTTCCCCCCCCCTATTAATATGAATCCCGCCCACACCCCCGCGGGGAAAAAGAGAGAGGGTGTGGTGCAGTCTTTTGGGGCCCCCCTCCCCTCTCTCTCCCCCCACATAGAAATCCCCTGCGGCGCTCTGCGTGCTCTCTGGTGGCGGGAAAAGGTGTATACTCTCTCTCCTCCTCAAGGGGGGATATCGCACGTGTGTCCCCCTAATCTGCGGAGAGATACCCCGAGAGAGAATAAATTTATACATCATCAGGGGCCCCAATGGGGCAAACACGCCTATAGGGCGC ++ 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+@230375c.t3 +CCGCGTTAATAAAATCTTCTTTTTAGGAATTTTTTTTTCAAGTGCCCCTATTCTTTATACAAAGTTGAAAAATGTACCATACTGCATTATTGCAAAAATTCACTGGTACAAAACACTTTGCAGCTGGTGAGAAGGCAATAAAAATTTGATTTTTAAACTCATTACTATAAATTATTCTTACAGTACTTTGCAAATTCAGAATTTCAAACTGCATGTTCTTTTTCTAAATTGCCCACAGTACTCGAGGTTCCTGAAGCTAAGGCAGCTGTTTCAAAGGAGGGGGAGGAGGTACCAAATGTCAAGGGATTTCCATTTCTCTTTCGATGCCGACATACTTCAGGGCATCACCCTGGCTGTATCTGTAATCAAAAAACAGCTCTTCACCACTCTGGATGGCTCTCTTGGGCAAAAAATACCAATCCGTTAATCACCCGTAAACCATTCCATTAACTTTTGGCAAAACCAATTTTTGGAAATTTCCCGAAAATAATTTTGCTCAAAACCCAAATTTTTGTTAACCCCCTGGGGGGGTTTTGCCCTCCCCCCCCCCCAATAATTCCCTTTGTTCCCAATTTTTTAAAACCAAAAAAACCCTGCCCCCACTGTTTTTTTTTTACCATAAACCCCTCCCCCCGTTGCCCCGAAATATTCCTTGGGCCCCCCAAAGGGGGCCCAAAAATTCCCCCAAAATGTGGGAATTCTCTTTTTTTAAAATTCCCTAAACCCCACTGTTTTCCCAAAACCTTTTTCCCCTCGTTTTTTAAGAGTTGTTTATATCCCGCCCCCCCTGTTTCCCCCCCTCCCTTTTCTAAACCGCGGAAAACCTTAAAAGTTTTTAAAACCCCGGGGGTTCTCCTCTCCTAAAATATTATACCCTCACCCCCCCTTTATAATTGTGCTTTCGTCCCTCCACACTGCGCCGCGTCCGTTCCCATTTCGGAAAAACACCTTCCTTTTCCCATATCCGCCCTTAAATAAATCGCGCTCACACCCCCCGCAGGGAAAAAGGGGAGTTTTTTATTTTTGCGGGCCTCTTCCCCCTTCTCTCTCCCCTAACAGAGATCTCTCTCGCTCTGTGTCTTTCCGGGTGCTGGGAAAAGGTTTTCTCATCCCTCTCCCAGGGGGGGTTCGGTGTTCTCCCATATATCGGGGAGATATACCCGAGAGAAAAATCTTTACACACTAGAGCGCGCCACAAGCGCGCAAAACTCGATGAGAGAGGGCGCCTCTTCTT ++ 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+@U13a03c03.t1 +XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTAACAAATCTCATGGTTTAAAAATTTCATAAAATTTCTCATTTCAAAAACGAGAAAATTAAGGCCTTGCGGGGTTAAATCGTTATCAAGTAATCAGTCGGCTCACTGCCCAGTGTGGACACTGGCCAATATTATGGCACCAGCCTTTGAGAAAAGGAAACCTTTTTTTGAATCCATCTCCCTGACCTGGGGTTTGGGTTGGGTTTTATCACCATAGGGTGACAGGCAAGTTCAATCTGATTGGATCCTGGATCCCATCATGGGGTATCTGTTCCTAAATCATTCCCTGATCCTCGGTCAGAGCGAGCGCTTAGGTTCCCGCTGCAGTTAAACACCTGGTTCATCTGGGCATACTAAGGTTATGACTTTCCACCTGGGAGTCCACGACAACTGAAAAAACTCAAAACTTCTTTAAGTAGAAGTTGAGCCTGAAGCTGAGGCAGCTGTTTCAGAGAGGAGGAGGAGGAGGAGATTGCTCATGTCCAGGGATTTCCATTTCTCTTTCAATGCCAACATACTTCAGGGCATCAGCCTGGCTGTATCTGTAATCAAAAAACAATTCTTCGCCAAGTCTGGATGGCTCTCCCTGAACAAAAAACACCTATCCCTGGTTGAATCACCCCATTAAACCCAATCCCTAAACTTTTTGGCCATAAACCAATTTTTGGGGAATTTTTCTCCCAAAAATTGAATATTTTGCCCAAAAAACCGCAAAAATATTTGTTGTTTTTAACCCCCCTCTTTGTCCCCGAGGGTGTTTTGCCCTCTTCCCCATCCCCCTCTCTAAAAAAAATTCATTTCTTTGTTTTCTCCAAAAAGTTTTTTGATAAAAACAAGAAAAAAAAGCGCCCCGCCCCTCCTCATTTGTTTTTTTTTTTTTATTTTACAACCACACCCACACCTTTTTTTCTCCCCTCTCCTCTCTCTCCCCCTTCTTCACCCCCCTCTTTTTCTCTTTTTTTGGGGGGGGGGAGAGAGAGAGAAAAAAAAATTTTTTCTCCT ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!;8777==----61511EAAE,=>=>>>@AE@====>AAEAEAAAAAAABA83:*3.1=>>:?>8;>?AB@?8;;??8@599,BB?@>AEEAAAAAAAAAAB826-8739:694?@F@ABBAAB???BEABABAABAD?@?BAA?AA?=?988:8?;;?>@?A865.;63797564889C@?>C5;BBA?AAA????A??@?A=@@@@ABCAA:====?D@?@AB????B?AAAABAAAAAAA?C??D@B>D<;804*5178:9@245188548AED@>?A8@?:@A@>?D???A@BB=<<<@;A<=?<:A?@@@?AB@@G??;9:1::9=:86/6?4792;;;EAAAAAAAAA?AAAEABAAAABBDAC1;1)62.72>??@82183*4+02)3737?;=D?=8+-7-5-162730;98:;2::/8:.*+(('+342.5.3;???A@@;8983545:;;?AA@;6/78;=;=>C0/,9/3++*)(40-<<>AA??D@@@@?ACA@BBC@A7:267.4,*35*+..3153,*(+-5+/),,,5.*)),,,40,+)*,,)**20-,,.+**)***-88-+2-+.-2<=32-*+)3-:.3+,/0)*,,-(,..*/.*)(/,..0/3/7/142+)))).,/582,*)()))-))//,))))++3)))))*1.0*')&+'+%''*22+)(((()+38,,))*)(()))((+()).()+*,&)*(&)&&),1)++/0,6.+,(&%,.5:15,*())(()+(+))))*,,),+,0325-'.12.,**,+,04,*&*+**-5@D1.*)+++.*)(,+)),''+''),-0-./946?<>>,))*,))+)0))()()),)),.5+,./,,4+.((''/,...()(,),((11592(.,)'))(,,*+11,**,,-)*+,1==A2/+5.-0;;:11*())','+.3/78;>??9;8:533752?C544;4148449@7<@@@;=866686AB@=====@==E==;;;@=>===B==@::;;:7ABB99?A??==;==?????AB??????AA??AAA==A========AA?B???@??A??ADCA@EE@@AAAAA======@??D@???BD?AAAAAA@=?C>:=?AAAAA??A===B???????D?@==<<@?AA?A???AC@BBAECAAA@@@C@@G@A@B@@B?????@AA@AC?=<52*/38@A??>B=====8=>A=B======AB=8=;>==>==C=>=A=B=>=BA??A??DAAAA??===B=9EEAA?=;<538A??<773766C?@@EEBA?A>=6;/3=?4;8689C<79251:378=9:8:@BEAAA?AA=:5*,85=89..43:5:G@AAAABA>====>=>=====E=?AA??>3;:8=8=D?=?=?E;17?=?@=73/3/268B=B844*+()*))49BB==:3.,*1,**,**,-*2,/2,3*,5./;;8==>56.2@6A===7681/.33*+-66632,(,*).**.31,)(&))*)**()*00.56.4.1/1/6C85526575,,0,,41-+((.8882//35BB2/,+,*)'+*/54)(0)+,**&).))&),*'%''))***)*.*(/,))1*)))%(%'')(,-,**),0,3,+*,*)%,/3&&&)844..+))'$))*****050/++*+)**%+***))**+*(+..**))+')()& 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+XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTGCAAAGTACTATAAGAATAATTTATAGCAATGAGTTTAAAACTCAACTTTTTATTGCCTTCTCACCAGCTGCAAAGTGTTTTGTACCAGTGAATTTTTGCAATAATGCAGTATGGTATATTTTTCAACTTTGAATAAAGAATACTTGAAATTGAAAAAAAAAATTGAGTCTGATGGGTCTAGTGTGTTTATAAAATGACTTAAGATCCCACAGTTATTTTAAAGTAATACATTACTCAACTGGTATTCATTTTGATGCCATTATTTTATTTTATAAAACTAGTCATCCTTGCAGAAGTGTATCTGATTAACTCTTGACAACTACTTTGCCTATTTTATTAACAGCTGCATTTAACCCACGTGACAGGATAACTAATTTCTATTGTTTTTGTATTTTTGCCTCCTCCTTCCAAGATAGCAGTAGAGTACTGTGTTAAATCTTGCTTCAGAAGAGCTTGTTTAAAATAGTTATAAAGAAAGTAAAATACATAGAAAAACACGTTATAATTTTAAATTAAAAAAGAAAAAAGATGTCTACTCTGAATAAATTATGCATACATATAAGGTCTGAACAAAAACATGAAAAGATGGGCTCTGAGTATCAATTTTAAAAATCTTTACCAGTATAACATTACTCAAACAAAAATTAAAATTTAATATAATTTAAGTACATATTCCAAGACAACCAATGGAACCTTGACTGTTAATTCTGGGAAAAGATCCC ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!DEEEAA=2?777;42;/73E;;=@=@@?@AA>==>=;?BB@@@AA?ABAAABAAAA@AEABAB?A==?@AEEBAAAAADBECCA========?7=3==AABDEEEEDADFA????DB?AAAAAAAE@=@==@@@@=BB==:@@>E?A?AAA?@@A=AAEFBEFE@?==@>;AA???;B==??A?A????AFCABCCDC?A?DAA@????DAA@DAAAAABABEEAAAABAAAA@@CD@BC@ED@A?>?@CBA?B=>>:@EEAAAACAAAAAABBAAABACD?AAA?????@A???8:=5:6;A@DA?AAAECAAA==>=:9ADABC@@==>>DAAAAABABAEEEAAAAABEDA?A:@=<@>A?===8==?ACEAAAAAABAA<>;;;ABAAAABA>@@AAAAEEE?AA;=>EAAAD?8A39:<==?????CCDAAB@@=:<=>880424?DADEBAAAEEEEBAABA??AAA?;?9??>@==8@ABBA=AA?@9:C;C;AA@DABCC@ADBEAAABAABBA@=B;;>????;=8<>>=@=AAAA@A><0.2-*30:82/)/,'*11=::A=@;42+99BD56-./(/+-BD@@=:==842?3/*,39=A??<<6.8)053;9AAAA??B?:611-*211*,3-0**.03;A4..56@B;:60.).)+)-.42,*(,*0)*&*1--1+-72054-+02?8:-,0.+,9(+22..'(,10 +@U13a04c06.t1 +XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXATTTTAAACAACCTCTTCTGAAGCAAGATTTAACACAGTACTCTACTGCTATCTTGGAAGGAGGAGGCAAAAATACAAAAACAATAGAAATTAGTTATCCTGTCACGTGGGTTAAATGCAGCTGTTAATAAAATAGGCAAAGTAGTTGTCAAGAGTTAATCAGATACACTTCTGCAAGGATGACTAGTTTTATAAAATAAAATAATGGCATCAAAATGAATACCAGTTGAGTAATGTATTACTTTAAAATAACTGTGGGATCTTAAGTCATTTAATAAACACACTAGACCCATCAGACTCAATTTTTTTTTTCAATTTCAAGTATTCTTTATTCAAAGTTGAAAAATATACCATACTGCATTATTGCAAAAATTCACTGGTACAAAACACTTTGCAGCTGGTGAGAAGGCCATAAAAAGTTGAGTTTTAAACTCATTGCTATAAATTATTCTTATAGTACTTTGCAAATTCAGAATTTCAAACGGCATTTTCTTTTTCTAAATTGCCCACAGTACTCGAGGTTCCTGAAGCTAAGCTGACGGAAGAGGGAAAGTGTGTGATAAATGCATGTGCAGCTTTCTGTTCAACTTGAACAATGATTTTGTGGTGGATGCAACCTGCAGGGTAACAAAATTCGTTTTGCAAATCATTCGGTAAATCCCAACTGCTATGCAAAATTTATGATGGTTAATGGTGATCACAGGATAGGTGTTTTTGTCAGGAGAACCCCCCCAGAATTGCGAAAGAAACTGTTTTTTTTGAATTACCGAATACCAGCCCAGGGCCGAATGCCCATGAAAATTATGTTTGGGCCTTTGAAAAAGAAAAAAATGGGGAAAATCCCCTTTGGACCATTTT ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!@@=B@:6;2@=,?647<>>ADB??:0,1..53392=A2711?AAABAAAAAAAAAB==;667.88,367;=9===867:AAB=A52)..0;;?@CC@???>AAC>@9@;;9>4:>@=8??@;?>>9>@BA??;;;9@;AD@8;5,75<@9/2*777<>A<4,*736AAAB=;;9;86:4:7187ABCDD?=?/*8;AAA:=:@859:?>AAA=B??@@@@@A@??49:5;=C<@=?????>???AAAAD=9>?;;?@==;;6586@8@???34+---58>@@B?:7-837::3+/29;;?C:9.977??7:;;?@>@@AAB?@??>?AA@B684-8@@@?@DAAA>>,*0;?>AB>B>A>A??86@@@B?@=???CGAAC@@@@EBB75;;=;:8415138=?D=78,/.*32:B>>@?;8888C@@@@@A????<6;>9;C=@?87:9:?ADD;74;AB?>@EBBB@A@AAA@;CA=C?7;578?@@@@=@@@@A:;4+486<7/--/2/.5/49?AAA;>7)99?>::7/41./1.75C?=0.)*-9BBAAADE@AAAAAA?????9;;;2;8==:<6=A?==:C<677=;==DA?1./*.1=:,024*,/285CCAA@@65543-)(/-/4=7/,).1)/,,-2)(.().+48./1**031;8==?<=002-*-./.71.976/.;;;BAB?<7-()(+,)+)+.+()12:*0*(2+,*-0156522/111;5;;=7//,)*(,*,/-+*+1'+09<0),)*()1-(('(,'++10.+61/3--+)+/./,*-*.376588773?:88*-11::515,20,,-+*(()(-+33A< +@U13a05b10.t1 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+(+/+*&)))+)))+)+10/79:*-))*.*(.,.***-6====A=>@E==A=>87;:BC<863)*;:A@?=7=CA??:746;BC?????;@=>=A>A993578@@=A?AAA==::=A=@@==?B=>=AAEAAAAB@>?AA?@FAC@BD?;;;??=@@===D==::4-6,25<=8;2<79@@B?;6;>==?984106<>??=0.+*/-/67AB@;5*.37:9==@?=.00*3.5;;;?@@;>4:==????CA;;.,,*-<2,+2,.2245===?A?9=?;>A6>6/669==B=?=<6853*708;873>39?.*)(1-2==:A9=:=?A@@=9<@@<9????>@@AA?;@5A?@@@-2*)23.664>C@:44.00465=<12;>56;4*+,3/*C;8@A???>><=CBA:8://011.)(,(*<1823...167,,)(21=286777551137943,))2.2-0>??+/;16;;GAA=1-.,+.:<6964626497?7:0084;9AC?AAAAA;;85>-53-1+77?:?;@C;???@7898;;=6::***,)*0/5+.463/.6774,1-8:?@AA=@;A-*4.84.37.,0).1(1;9@;:,(1**314,+,+)25,*))-+*/--**((+(0//*---*(*++)01--1*,(()(),-?311'+.))'(()17:6-++(+*%,19-(**)*-&'+*..(+**((,*,0))+)()0/ +@U13a06d03.t1 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+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!@A???>??893;5.8;?B?C;=;====;88;=CAAA==961/9.5.5=7::>=8:=75:6/34-6;?A@??;<,6625777:5:4:C;?DAAAAAAAADAAACDB@@EAF@A>??EDBBFDGCAAAAF@DA@B?=AC?DAACCC@?@@AAEEEDAAA@@A;;>7==?=@==A=>==A?AAEB@??;???CC?32(*).66/8??AAABAC@EAAA=ACBAAB??AAA?97+799B@=?=A?@==B;=====?EA@@@?B@=B=A@A?A?AABAABB??A????BAA?B??=BB?::8:=9DD:=9:?5:838<@@?;??;AAACD?FACEA??AAACC@@CF?D?CA?CD?@A??;6??BBA>==6??A?B======>@<;4:=A:=====????AAAAAA?6:=63*3?9>/86:??B?8??>?9A>=B16;9:=?>DA?D@A?C<6<=C==AAAAAA?BB89448=C=AAABD@?A???CAAAC@95778;?CABCA6.5--2+*3,495;>==51+*.()+.+,57;?AAAA@AA@@8/1((21/32,*51345514*)(21./3/00+/,-))),-*,0))11:87?6941355)),'*)))'*,(*()-*),)+-*,+)((+,+1.::42+.-(+.,6*-+(*+53-.3.,.(*(+)6.+)**,**)(,,2*+5+(*)).*'0**1+*(*,+-2-01/)*)))-+)))(),()*,).,2)+,.03.+)$')'-2*..-)*+)()-+0056))*-6+))))))))/..(++*-))&& +@U13a08b04.t1 +CCTCGATCTAGAGGACCCTCTCCTGACAAAAACACCTATCCTGTGATCACCATTAACCAXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX ++ +(),**+(,/+*.**'&**;;B===6:4/A4266385;===@AB453355==B?7476<;!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! +@U13a08f10.p2 +XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTAACAAATCATCAGTGGTTTAGAAATTTCATAAAATTTCTCATTTCAAAAACGAGAAAATTAAGGCCTTGCGGGGTTAAATCGTTATCAAGTAATCAGTCGGCTCACTGCCCAGTGTGGACACTGGCCAATATTATGGCACCAGCCTTTGAGAAAAGGAAACCTTTTTTTGAATCCATCTCCCTGACCTGGGGTTTGGGTTGGGTTTTATCAGCATAGGGTGACAGGCAAGTTCAATCTGATTGGATCCTGGATCCCATCATGGGGTATCTGTTCCTAAATCATTCCCTGATCCTCGGTCAGAGCGAGCGCTTAGGTTCCCGCTGCAGTTAAACACCTGGTTCATCTGGGCATACTAAGGTTATGACTTTCCACCTGGGAGTCCACGACAACTGAAAAAACTCAAAACTTCTTTAAGTAGAAGTTGAGCCTGAAGCTGAGGCAGCTGTTTCAGAGAGGAGGAGGAGGAGGAGATAGCAAATGTCAAGGGATTTCCATTTCTCTTTCAATGCCAACATACTTCAGGGCATCAGCCTGGCTGTATCTGTAATCAAAAAACAGTTCTTCGCAAGTCTGGATGGCTCTCCTGACAAAAACACCTATCCTGTGATCACCATTAACCATCATAACTTTTGCATAGCAGTTTGGATTTACCGAATGATTTGCAAAACGAATTTTGTTACCCTTGCAGGTTGCATCCACCACAAAATCATTGTTCAAGTTGAACAGAAAGCTGCACATGTATTTATCACACACTTTCCCTCTTCCGTCAGTTTAGCTTCAGGAACCCCGAGTACTGTGGGAATTTAGAAAAGAAAATGCCGTTTGAAATTCTGAATTTGCAAAGTACTATTGAGATTATTTATCGCAATGAGTTTAAAACCCACT ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!?;=;F@844AA4=@7AAAAAAAA@??@??B?=?==@====?===>=??AAAAA?B;54/14=BACABBABA====@:=?===AAAA?BAAA?AAA@======??>AAAB@8::==>F?>?DA?AAAAABBB???ACDFA@BAABB@>@>@DEEA@@?????AAAAAB<@;9=@A===;=AA=5====AAAAAAAAA???=@=>>?=;=???A?====??@C@>@@AAAAAAA??AA@====@AG??:<61<@@@@@@@AAAAAAAAAAAA?645/.5A=::87;?AB:=;::D@?>??@8B?;331747?A=;==>E====@;A??E@?==8@=;;BA=>;=:9==44==;=??AA<:=9<6:???AAA;;841581/78;6;166:9?E?>@==9;98;9;=;92:/88====>==>?A:0575:;=====:EAA======AABAB62199==98===;544/6;6=4/3**35;5:;A9/()**0;0**,,-2;:?;;7-,+*-(,,,3555.*+-63;0+.,*(,+6892/.)*/),15?9-+))17=====@810(),-64-0/..**13*&(*,)(%)*--;3713-4.+(()),.,+/-+,*,,/389-'*)*(,)2A04,1./+,*/+)+)&&*.*)+)(()0/21**-.)((($(%)((++**+*-//(*())(((0(*(.*'%**))-++' +@U13a08f11.t1 +GGGAGTGCACTCGATCTAGAGGACCCTATTTATCACACACTTTCCCTCTTCCGTCAGCTTAGCTTCAGGAACCTCGAGTACTGTGGGCAATTTAGAAAAAGAAAATGCCGTTTGAAATTCTGAATTTGCAAAGTACTATAAGAATAATTTATAGCAAGGAGTTTAAAACTCAACTTTTTATTGCCTTCTCACCAGCTGCAAAGTGTTTTGTACCAGTGAATTTTTGCAATTAATGCAGGTATGGTTATATTTTTTCAACCTTTGAATCAAAGGAATACTTTGCAAATCTGGAAACAATAACTATACTTTAAGTCTGAAACTCTGTTCCTGGATGTCGTTTTAATAAAAATATGGACCTTCAACGAATCCCCCACATAGCTTTAATTTTTAAGAAGTTTAAGATACAACATCTTCGACCTTCAAAACTGGGTTAGATATCTCTATTCTTTGGATGGCCCACTTATATTGTCTCTCAGATCTTCTTCTATTACATAACTAATAGCGTCCGGTTCTCACTCTCTCTCTCGACCAGCGAAGGTATGCTGTGCCCTGGAATTGAATACCTCCTTTCGGAACACTACACTGCTACTTTATGGCCCTTATACTTATATAATCTTATATCACTATGAGCCTGGCCATATCTTACACCGCGCGCAGACGGTTGAGAACAGACGATAAGACCACTACACATCTATTCTCATAGATTTGTTTCTATCTGAGTATGATATCTTCTCTGAGCCTCTCCACTCTCCCTTCTCCGAATGAGGCAATATAGCGCACGATGCTCAGAGAAGCGTAGTCGCGTGGTTGGTTTCTCGATAGATCCTCTTCGCCCTCTCTCATGACAAAAGCGAAGCACTCTTGTTCTCTGAACGAGAGTCTAGCTGTCTTTACCAGAGACGGAAATGAGTTGTACTAAATTATACTCTACTCTCGTCCATAAGCATCAGCCGCGCCGTCTCTTATCGCACATCTCTGCTCTCTCAATAGCTATCGTGCATGTATACACAGAGAATAGATCATGCATGTACTCGTATATACGTTATGTCATCACTCTCTCTGCGTAACACATGACGATATCTGCTGATCTGCGCGATCATCTCTCTATTCATATATCATGATAGGGTCGTCTGTGAACACATCACATACTCATCTTATCGCGAGAA ++ 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+@U13e07d02.t2 +XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXATTTTATACTTTTAGGCACTACTGGTCAAAGTATTTGGGATCTTTTCCAGAATTAACAGTCAAGGTCCATTTGTTGTCTTGGAATATGTACTTAATTATATTAAATTTTAATTTTTGTTTGAGTAATGTTATACTGGTAAAGATTTTTAAAATTGATACTCAGAGCCCATCTTTTCATGTTTTTGTTCAGACCTTATATGTATGCATAATTTATTCAGAGTAGACATCTTTTTTCTTTTTTAATTTAAAATTATAACGTGTTTTTCTATGTATTTTACTTTCTTTATAACTATTTTAAACAAGCTCTTCTGAAGCAAGATTTAACACAGTACTCTACTGCTATCTTGGAAGGAGGAGGCAAAAATACAAAAACAATAGAAATTAGTTATCCTGTCACGTGGGTTAAATGCAGCTGTTAATAAAATAGGCAAAGTAGTTGTCAAGAGTTAATCAGATACACTTCTGCAAGGATGACTAGTTTTATAAAATAAAATAATGGCATCAAAATGAATACCAGTTGAGTAATGTATTACTTTAAAATAACTGTGGGATCTTAAGTCATTTTATAAACACACTAGACCCATCAGACTCAATTTTTTTTTTCAATTTCAAGTATTCTTTATTCCAAGTTGAAAAATATCCATACTGCATTATTGCAAAAATTCACTGGTACAAAACACTTTGCAGCCGGGTGAGAAGGCCATAAAAAATTGAGTGTTTAAACTCATTGCTATAAATTATTCTTATAGTTCTCTTGCCAATTTCGAAATTTCAAACGGGCCTTTTCTTTTTTCTAAATTGCCCACCGTTTCCCGAAGGTTCCTGAAACCAAACTGAACGGAAGAAGGGAAAGTGTGTGAATAACTC ++ +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!=9=;49.-,,66,2(*18=56--1A;CEC?4787@D?EAEB894+75??BD?AAAAA??@=B=@?A??B???ABBEAAAABA@@@?CCFBBBAC@A>???>;AA@ACA?;8817AA?=;8;58?DDBAAAC???>CC93.*9.8CAAABAEDA@>D????A@??5:94>?:@BAA=??A?CDA@CCAB@AADC??97176/6;1?ADABAAAAAADAAAAEAAAAAAAAAAAAD??@??@DDAAA??8===?AAAAAAAADAAABABBBCAADAADDFAD@?CADDD?=A<5;2686==AAAC@AA@DDFCAFD??;;:8AA=>@:=9:==>>=88:+363?=;?@@EDFAAAAA?AA?AA??AAA===C?;>AD9::646+6>2>806669>@??;8@???@=<<;@;E@D@AABAD>=>>=@===AAAEFFAAAAAAA??59?=@?20)),.7<@DC>==9=>A@;6532748?@@;<5<==A;==8==61**0-12173>@<@=A@293581..2988:61*25:/5+,*24.,.+(+))*(-*(,))-)(-*(9,,,,(*.6@AA>-/-/((),+23;67>61)()(*()****,5:>A8;-,-*())))+))),,-,*+*,%15*43,+)))*(-3+,,65,*++,/-+((+,.36-4,+)+((0,())+&3*.)*++**)/4(5/(3..*)-/0453315702**-*14*-+/+(+.*((++ +@U13e07f02.t2 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diff -r 4c6e4d583b8f -r 5bbaa930d7fa test-data/U13small_m.mira4_de_novo.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/U13small_m.mira4_de_novo.fasta Mon Mar 03 11:49:21 2014 -0500 @@ -0,0 +1,47 @@ +>MIRA_rep_c1 +aaatttcataaaatttctcatttcaaaaacgagaaaattaaggccttgcggggttaaatc +gttatcaagtaatcagtcggctcactgcccagtgtggacactggccaatattatggcacc +agcctttgagaaaaggaaacctttttttgaatccatctccctgacctggggtttgggttg +ggttttatcagcatagggtgacaggcaagttcaatctgattggatcctggatcccatcat +ggggtatctgttcctaaatcattccctgatcctcggtcagagcgagcgcttaggttcccg +ctgcagttaaacacctggttcatctgggcatactaaggttatgactttccacctgggagt +ccacgacaactgaaaaaactcaaaacttctttaagtagaagttgagcctgaagctgaggc +agctgtttcagagaggaggaggaggaggagatagcaaatgtcaagggatttccatttctc +tttcaatgccaacatacttcagggcatcagcctggctgtatctgtaatcaaaaaacagtt +cttcgcaagtctggatggctctcctgacaaaaacacctatcctgtgatcaccattaacca +tcataacttttgcatagcagtttggatttaccgaatgatttgcaaaacgaattttgttac +ccttgcaggttgcatccaccacaaaatcattgttcaagttgaacagaaagctgcacatgt +atttatcacacactttccctcttccgtcagcttagcttcaggaacctcgagtactgtggg +caatttagaaaaagaaaatgccgtttgaaattctgaatttgcaaagtactataagaataa +tttatagcaatgagtttaaaactcaactttttattgccttctcaccagctgcaaagtgtt +ttgtaccagtgaatttttgcaataatgcagtatggtatatttttcaactttgaataaaga +atacttgaaattgaaaaaaaaaattgagtctgatgggtctagtgtgtttataaaatgact +taagatcccacagttattttaaagtaatacattactcaactggtattcattttgatgcca +ttattttattttataaaactagtcatccttgcagaagtgtatctgattaactcttgacaa +ctactttgcctattttattaacagctgcatttaacccacgtgacaggataactaatttct +attgtttttgtatttttgcctcctccttccaagatagcagtagagtactgtgttaaatct +tgcttcagaagagcttgtttaaaatagttataaagaaagtaaaatacatagaaaaacacg +ttataattttaaattaaaaaagaaaaaagatgtctactctgaataaattatgcatacata +taaggtctgaacaaaaacatgaaaagatgggctctgagtatcaattttaaaaatctttac +cagtataacattactcaaacaaaaattaaaatttaatataattaagtacatattccaaga +caacaaatggaccttgactgttaattctgg +>MIRA_rep_c2 +gcaatatcgtgacgatatgtawgataaatacatgtgcagctytctgttcaacttgaacaa +tgattttgtggtggatgcaacccgcaagggtaacaaaattcgttttgcaaatcattcggt +aaatccaaactgctatgcaaaagttatgatggttaacggtgatcacaggatakgtatttt +tgccaagagagccatccagactggcgaaragctgttttttgattacagatacagccaggc +tgatgccctgaagtatgtcggcatcgaaagagaaatggaaatcccttgacatctgctacc +tcctccccctcctctgaaacagctgccttagcttcaggaacctcgagtactgtgggcaat +ttaaaaaaagaacatgcagtttgaaattctgaatttgcaaagtactgtaagaataattta +tagtaatgagtttaaaaatcaactttttattgccttctcaccagctgcaaagtgttttgt +wccagtgaattttgcaataatgcagtatggtacattttcactttgaataaagaatacttg +a +>MIRA_rep_c3 +gcgttattaaagacttttttttwtttttttttcaagttcaagtattctttattcaaagtt +gaaaaatgtaccatactgcattattgcaaaaattcactggtacaaaacactttgcagctg +gtgagaaggcaataaaaagttgatttttaaactcattactataaattattcttacagtac +tttgcaaattcagaatttcaaactgcatgttctttttctaaattgcccacagtactcgag +gttcctgaagctaaggcagctgtttcagaggagggggargaagtaycaaatytcwaggga +tttccatttctctttccatgccgamatacttcagggcatcagcctgactgtmtctgtaat +caaaaaacakctcttcgccavtctggatggctctctyggcaaaaatacctatcctgtgat +caccgttaaccatcataacttttgcatagcattt diff -r 4c6e4d583b8f -r 5bbaa930d7fa tools/mira4/README.rst --- a/tools/mira4/README.rst Tue Feb 25 13:13:17 2014 -0500 +++ b/tools/mira4/README.rst Mon Mar 03 11:49:21 2014 -0500 @@ -98,7 +98,7 @@ For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder:: - $ tar -czf mira4_wrapper.tar.gz tools/mira4/README.rst tools/mira4/mira4_de_novo.xml tools/mira4/mira4_mapping.xml tools/mira4/mira4_bait.xml tools/mira4/mira4.py tools/mira4/mira4_make_bam.py tools/mira4/mira4_validator.py tools/mira4/mira4_bait.py tools/mira4/tool_dependencies.xml tools/mira4/repository_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta test-data/tvc_map_ref_strain.fasta test-data/tvc_map_same_strain.fasta test-data/tvc_bait.fasta test-data/tvc_mini_bait_pos.fastq test-data/tvc_mini_bait_strict.fastq test-data/tvc_mini_bait_neg.fastq test-data/ecoli.fastq test-data/ecoli.mira4_de_novo.fasta test-data/empty_file.dat + $ tar -czf mira4_wrapper.tar.gz tools/mira4/README.rst tools/mira4/mira4_de_novo.xml tools/mira4/mira4_mapping.xml tools/mira4/mira4_bait.xml tools/mira4/mira4.py tools/mira4/mira4_make_bam.py tools/mira4/mira4_validator.py tools/mira4/mira4_bait.py tools/mira4/tool_dependencies.xml tools/mira4/repository_dependencies.xml test-data/U13small_m.fastq test-data/U13small_m.mira4_de_novo.fasta test-data/tvc_mini.fastq test-data/tvc_contigs.fasta test-data/tvc_map_ref_strain.fasta test-data/tvc_map_same_strain.fasta test-data/tvc_bait.fasta test-data/tvc_mini_bait_pos.fastq test-data/tvc_mini_bait_strict.fastq test-data/tvc_mini_bait_neg.fastq test-data/ecoli.fastq test-data/ecoli.mira4_de_novo.fasta test-data/empty_file.dat Check this worked:: @@ -113,6 +113,8 @@ tools/mira4/mira4_bait.py tools/mira4/tool_dependencies.xml tools/mira4/repository_dependencies.xml + test-data/U13small_m.fastq + test-data/U13small_m.mira4_de_novo.fasta test-data/tvc_mini.fastq test-data/tvc_contigs.fasta test-data/tvc_map_ref_strain.fasta diff -r 4c6e4d583b8f -r 5bbaa930d7fa tools/mira4/mira4_de_novo.xml --- a/tools/mira4/mira4_de_novo.xml Tue Feb 25 13:13:17 2014 -0500 +++ b/tools/mira4/mira4_de_novo.xml Mon Mar 03 11:49:21 2014 -0500 @@ -151,7 +151,7 @@ @@ -159,9 +159,11 @@ + + + - --> - diff -r 4c6e4d583b8f -r 5bbaa930d7fa tools/mira4/mira4_mapping.xml --- a/tools/mira4/mira4_mapping.xml Tue Feb 25 13:13:17 2014 -0500 +++ b/tools/mira4/mira4_mapping.xml Mon Mar 03 11:49:21 2014 -0500 @@ -157,27 +157,30 @@ - -