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u}Uɉu}EuEϋuUu9v9щ1 v9vL11ɉȋMt؃ڃ ^_]Í&u 1ƋM1lj뾍ЃUuE;uv9s1뛍vuڃES]UU]At&ME +EM UuMUU ׉u։e9։Ur UM9s;ut1t&O1U]Ít&'UWVSO8)t$1ED$E D$E$9rރ[^_]Ë$ÐUS t fЋu[]ÐUS[l8Y[twoBitToFa - Convert all or part of .2bit file to fasta usage: twoBitToFa input.2bit output.fa options: -seq=name - restrict this to just one sequence -start=X - start at given position in sequence (zero-based) -end=X - end at given position in sequence (non-inclusive) -seqList=file - file containing list of the desired sequence names in the format seqSpec[:start-end], e.g. chr1 or chr1:0-189 where coordinates are half-open zero-based, i.e. [start,end) -noMask - convert sequence to all upper case Sequence and range may also be specified as part of the input file name using the syntax: /path/input.2bit:name or /path/input.2bit:name or /path/input.2bit:name:start-end must specify -seq with -start and -endcan't specify both -seq and -seqListw%s:%s:%d-%d%s:%sseqstartseqListnoMaskfalsetrue: %ld millis
fclose failed%s%sError reading %lld bytes: %sCouldn't read stringError writing %lld bytes: %s to read to write to appendCan't open %s%s: %sn/abuffer overflow, size %lld, string size: %lldbuffer overflow, size %lld, new string size: %lldbuffer overflow, size %lld, substring size: %lldbuffer overflow, size %d, format: %sOut of memory in readline - request size %d bytesString too long in writeString (%d chars): %sCan't take median of empty list.{{?dnaseq.cInternal error %s %doffset <= inSeq->sizeactualSize <= inSize/3+1translateSeqNdnautil.cval >= 0 && val < 64tttttcttattgtcttcctcatcgtattactaatagtgttgctgatggcttctcctactgcctcccccaccgcatcaccaacagcgtcgccgacggattatcataatgactaccacaacgaataacaaaaagagtagcagaagggttgtcgtagtggctgccgcagcggatgacgaagagggtggcggagggcysteineaspartic acidglutamic acidphenylalanineglycinehistidineisoleucinelysinemethionineasparagineprolineglutaminearginineserinethreoninevalinetryptophantyrosinevalToCodon?errabort.cERRASSERTERRABORTToo many popAbortHandlers Too many popWarnHandlers %s %sToo many pushAbortHandlers, can only handle %d Too many pushWarnHandlers, can only handle %d debugAbortexpandFaFastBuf: integer overflow when trying to increase buffer size from %u to a min of %u.No name in line starting with '>'Invalid fasta format: sequence size == 0 for element %sExpecting sequence name after '>' line %d of %s>%s can't open %sread of fasta file failedfseek on fasta file failedExpecting '>' line %d of %s%s duplicated in %shash.c%s not found%s duplicated, abortingpowerOfTwoSize <= 24 && powerOfTwoSize > 0attempt to remove non-existant %s from hashnewHashShort line %d of %sUnexpected end of file in %sError line %d of %s: Couldn't lineFileSeek %s.gz.Z.bz2linefile.cnewSize > lf->bufSizeHTTP/discarding footer line: %s 200Transfer-Encoding: chunkedContent-Length:Premature end of file in %sBZsomefile.%sCouldn't open %s , %sbzip2-dccompressgzipExpecting at least %d words line %d of %s got %dExpecting %d words line %d of %s got %dExpecting double field %d line %d of %s, got %sExpecting number field %d line %d of %s, got %sCan't lineFileSeek on a compressed file: %sLine too long (more than %d chars) line %d of %s%s: chunked transfer-encoding chunk size parse error. %s: chunked transfer-encoding: expected blank line, got %s %s: chunked transfer-encoding: got footer %s, discarding it. %s: Expecting HTTP/ header line, got this: %s %s: Errored HTTP response header: %s %s %s lineFileExpandBufCouldn't allocate %lld bytesneedHugeMemResize: Out of memory - request resize %llu bytes needHugeMem: trying to allocate 0 bytesneedHugeMen: Out of huge memory - request size %llu bytes needLargeMemResize: trying to allocate %llu bytes (limit: %llu)needLargeMemResize: Out of memory - request size %llu bytes needLargeMem: trying to allocate %llu bytes (limit: %llu)needLargeMem: Out of memory - request size %llu bytes memTrackerEnd without memTrackerStartBad start cookie %x freeing %llx Bad end cookie %x%x%x%x freeing %llx Bad start cookie %x checking %llx Bad end cookie %x%x%x%x checking %llx Loop or more than 10000000 pieces in memory listAllocated too much memory - more than %s bytes (%s)needMem: trying to allocate %llu bytes (limit: %llu)needMem: Out of memory - request size %llu bytes multiple memTrackerStart callsToo many popMemHandlers()obscure.cdotMod > 0%lld,%03lld,%03lld,%03lld%lld,%03lld,%03lld%lld,%03lld%lldUnmatched %cmissing closing %c in %sfile read failedfile write failedCouldn't open %s. %s Write error on %s. %s rbr+bwbline %d of custom input: variable needs to start with letter '%s'line %d of var %s in custom input: %s missing = in var/val pairline %d of input: missing closing %cdotForUserInitoptGet called before optionHashMissing required command line flag %sERROR: optionMultiVal can only be used after optionInit is called with a non-NULL optionSpecsvalue of -%s is not a valid double: "%s"value of -%s is not a valid float: "%s"ERROR: optionVal cannot be used to get the value of an OPTION_MULTIvalue of -%s is not a valid long long: "%s"value of -%s is not a valid integer: "%s"boolean option -%s must not have valuestring option -%s must have a valueint option -%s must have a valuefloat option -%s must have a valuedouble option -%s must have a valuebug: invalid type in optionSpec for %sUNIMPLEMENTED: multiple instances of a non-string option is not currently implemented--http://-%s is not a valid optionverbosefstat failedCouldn't do tcgetattrCouldn't do tcsetattrI/O errorCouldn't do tcsetattr2Unable to forkmysqlHostMYSQLHOSTCouldn't make directory %s..stat failed in listDirXUnable to set dir %sNo current directoryHTTP_HOSTunknown%s_%s_%x_%x%s/%s%d%scan't get user name for uid %dstat failed in fileModTime: %s%s is not in %s%s %d %d .2bit,twoBit.cpEnd <= 4pStart >= 0%s is truncatedname %s too longinvalid twoBit sequence specification: "%s"twoBitReadSeqFrag in %s end (%d) >= seqSize (%d)twoBitReadSeqFrag in %s start (%d) >= end (%d)%s doesn't have a valid twoBitSigCan only handle version 0 of this file. This is version %dError in faToTwoBit, index overflow at %s. 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m-crtstuff.c__CTOR_LIST____DTOR_LIST____JCR_LIST____do_global_dtors_auxcompleted.7065dtor_idx.7067frame_dummy__CTOR_END____FRAME_END____JCR_END____do_global_ctors_auxtwoBitToFa.coptionscommon.cdoubleCmpintCmpnaStremptyStrlastTime.9858dnaseq.c__PRETTY_FUNCTION__.7757dnautil.cfindTailPolyAMaybeMaskinitNtValinittedNtValinitNtCharsinitted.7588initNtCompTableinittedCompTableopened.8250initted.7601findHeadPolyTMaybeMask__PRETTY_FUNCTION__.7557errabort.cwarnIxwarnArraydefaultVaWarndebugAbort__PRETTY_FUNCTION__.7282defaultAbortabortIxabortArraywarnAbortHandlerfa.cexpandFaFastBuffaFastBufSizefaFastBufname.8207nextSeqFromMemname.8311faReadAllMixableInLffaReadAllSeqMixablehash.c__PRETTY_FUNCTION__.7759linefile.cdetermineNlTypemetaDataAddgetDecompressorGZ_READ.8031Z_READ.8032BZ2_READ.8033__PRETTY_FUNCTION__.8195localmem.cnewBlockmemalloc.cmhStackdefaultMemHandlermaxAlloccarefulAllocedmemTrackercarefulMaxToAlloccarefulAlignSizecarefulAlignAddcarefulAlignMaskcarefulMemHandlercarefulParentmemTrackerFreememTrackerAllocmemTrackerRealloccarefulFreecarefulAlloccarefulReallocdefaultReallocdefaultFreedefaultAllocobscure.cdot.8198_dotForUserMod__PRETTY_FUNCTION__.8193options.coptGetoptionSpecificationmatchingOptionparseOptionscommonOptionssetOptionsosunix.chostBuf.7877host.7876dir.7511origSec.7482hostName.7853unamebuf.7855buf.7854name.7893fileName.7907twoBit.cpackedSizefindGreatestLowerBoundtwoBitSeekToreadBits32readBlockCoordsparseSeqSpec__PRETTY_FUNCTION__.8398verbose.clogVerbositycheckedDotsEnabledlogFiledotsEnabledwildcmp.cpipeline.ccheckOptsjoinCmdsafeCloseclosePipeline__PRETTY_FUNCTION__.8233plProcNewpipelineNewmemPseudoCmd.8284pipeCreatechildAbortHandlerplProcSetuppipelineExecpipelineStartReadopenWritebits.cinittedBitsInByteoneBitrightMaskleftMaskdlist.cdlNodeCmpcompareFuncdystring.cdyStringExpandBuf__PRETTY_FUNCTION__.7234_GLOBAL_OFFSET_TABLE___init_array_end__init_array_start_DYNAMICfileno@@GLIBC_2.0maskFromUpperCaseSeqgetHostdlListToSlListdata_startcmbStartCookieabort@@GLIBC_2.0__errno_location@@GLIBC_2.0pipelineOpenFdsubCharlineFileOpenintronOrientationshuffleArrayOfPointersbitClearOnetwoBitWriteOneslIntCmplmSlNameskipToSpacesslPairNewhashMustFindNamevaWarnreverseUnsignedslLastElcarefulCountBlocksAllocatedslNameInListgetpid@@GLIBC_2.0slSortcloneLongStringmkdir@@GLIBC_2.0needLargeZeroedMemstrerror@@GLIBC_2.0lineFileNeedDoublecreat64@@GLIBC_2.1digitsBaseTentranslateSeqNdyStringAppendMultiCbitCountRangereverseDoubles__libc_csu_fininaForNullsplitOffNumberrangeIntersectionrefListFromSlListslNameAddHeadmustReadqsort@@GLIBC_2.0valToNtMaskedpopWarnHandlerslPopTail_startdlListInithashStoreNamecodonTabledyStringResizewriteSeqWithBreakscountWordsInFileunpackDnaopen64@@GLIBC_2.1nextQuotedWordpackDna4mustOpentwoBitWriteHeaderoptionParseIntoHashtoggleCasebitClonefaReadNextptToSizetpackDna8slPairFreeListptArrayIxrefAddUniquedotForUserverboseSetLevelfaReadAllPeplineFileDecompressFd__fprintf_chk@@GLIBC_2.3.4lineFileExpectAtLeastunpackDna4readString__gmon_start___Jv_RegisterClassesdoubleSortverboseLogFilepipelineDescpopAbortHandlerhashIntValDefault_fp_hwrealloc@@GLIBC_2.0hashAddNntCharsrewind@@GLIBC_2.0bitAnddyStringAppendEscapeQuotestwoBitClose__xstat64@@GLIBC_2.2lineFileNeedNumoptionInitslDoubleCmptwoBitFromFile__printf_chk@@GLIBC_2.3.4bitsInBytefastReadStringfaReadAllMixedntValNoNswapBytesdnaFilteredSizeverbosefileModTimestrtod@@GLIBC_2.0strchr@@GLIBC_2.0getenv@@GLIBC_2.0safecat_finifaFreeFastBufgentleFreepipelineOpen1strncpy@@GLIBC_2.0lineFileParseHttpHeaderdlCountnewDnaSeqlmAllocnextWordslNameCmpCasecloneStringgetCurrentDirwrite@@GLIBC_2.0dlEmptyhashElListHashwildMatchfaFromMemTextfaReadOneDnaSeqfreeDlListcodonValtwoBitSpecFreebitReadOnecloneStringZslNameFindwantMemnullIfAllSpacefgets@@GLIBC_2.0isStopCodonbitFreeisKozakmemset@@GLIBC_2.0endsWithfopen64@@GLIBC_2.1dyStringAppendbitClearmakeEscapedStringintAbsbyteSwap32hashNextNamefileSizednaScoreMatchfreeDlListAndValscopyFilespaceOutchopSuffixbitClearRange__libc_start_main@@GLIBC_2.0twoBitSeqSizeNoNslineFileShortbitXorfaSeqListFromMemTextRaw_IO_getc@@GLIBC_2.0__memcpy_chk@@GLIBC_2.3.4dotForUserInithashLookupslPairFreeisAllDnachopPrefixAtstrrchr@@GLIBC_2.0startsWithclEndslNameCmptoUpperNoptionMultiValuname@@GLIBC_2.0trimSpacesbitPrintpipelineOpenFd1tcgetattr@@GLIBC_2.0hashFreeListbitSetRangefseeko64@@GLIBC_2.1hashLookupNextpositiveRangeIntersectionclStartslReverse__assert_fail@@GLIBC_2.0lineFileDecompressMembitReallocsplitOffNonNumericuglyTimereverseBytescloneMemhashMayRemovelineFileStdincomplementhashAddUniqueslPairFindValhashWordsInFile__vsnprintf_chk@@GLIBC_2.3.4cmpFileInfontMixedCaseCharstouppersread@@GLIBC_2.0hashAddSaveNamentValLowerstrtoll@@GLIBC_2.0optionLongLongtwoBitFromDnaSeqperror@@GLIBC_2.0slPairFreeValsAndListlineFileAbortpipelineOpenMembitFindslNameStoreungetc@@GLIBC_2.0ntValMaskedskipIgnoringDashaaScore2optionMustExistnewDyStringincCounterFilepushDebugAbortnextTabWorddlCatlineFileNext_IO_stdin_usedgettimeofday@@GLIBC_2.0reverseIntRangemakeDirntCompTablefreeDyStringListstrtol@@GLIBC_2.0fdopen@@GLIBC_2.1__ctype_toupper_loc@@GLIBC_2.3rStringInfaReadAllMixedInLfisPipentValUpperfree@@GLIBC_2.0noMaskneedHugeZeroedMemResizefaPepSpeedReadNexthashOptionalValsleep1000stripChardlAddTaillineFileLongNetReadlowerToNslDoubleNewrefAddmakeDirswriteBits64lineFileChopCharNext__data_startchopByWhitesigaction@@GLIBC_2.0fflush@@GLIBC_2.0containsStringNoCaseslNameFindIxhashCrchashFindVal__vfprintf_chk@@GLIBC_2.3.4dnaMixedCaseFilteroutputOnehashNextlineFileSetUniqueMetaDatabitSetOneopendir@@GLIBC_2.0newFileInfodlRemoveHeadfaSeqFromMemTextslPopHeadfaReadMixedNextintronOrientationMinSizedyStringCannibalizedup2@@GLIBC_2.0twoBitOpen__ctype_b_loc@@GLIBC_2.3optionHashSomedlGetBeforeHeadfseek@@GLIBC_2.0hashRemoveintToPtslUniqifyslNameAddTailslSafeAddHeadsafefisatty@@GLIBC_2.0hashReplaceerrAborthashStringfclose@@GLIBC_2.1valToCodonpipelineFreefaReadAllIntoHashdnaBaseHistogramftello64@@GLIBC_2.1dnaOrAaFilterlineFileCloseListfaWriteAllbitAllocmustReadStringhashMustRemovespaceToUnderbarfaSpeedReadNextlineFileExpandBufzeroBytesnewSlNamelmCloneStringtailPolyASizeLoosefreeHashstripStringreaddir64@@GLIBC_2.2safecpyclock1000dyStringAppendClineFileChopNextstderr@@GLIBC_2.0hashTraverseElsmemcpy@@GLIBC_2.0twoBitReadSeqFragLowerchopSuffixAtpushWarnHandlerchopStringdlInsertBetweenexecvp@@GLIBC_2.0mustWritedlAddAftercountSamednaTranslateSomenewDlListdyStringPrintfdlPopTailcpFilestripCommasdlRemoveTaillineFileExpectWordshashElCmpdlSortreverseUnsignedRangegetpwuid@@GLIBC_2.0translateSeqoptionExistswhiteSpaceChopperlineFileChopNextTabmakeQuotedStringpushMemHandlerstrstrNoCasetoLowerNtwoBitReadSeqFragExttwoBitIsRangeslAddTail__dso_handleneedHugeMemwaitpid@@GLIBC_2.0skipToNumericlineFileSeekfgetc@@GLIBC_2.0memTrackerEndbitOrstrcpy@@GLIBC_2.0emptyForNulllineFileOnStringcarefulCloselineFileNextRealpopMemHandler__DTOR_END__eraseTrailingSpaceshashLookupUpperCase__libc_csu_initnewHashhashElFreelmInitreadLinenaForEmptydyStringVaPrintfpushAbortHandlermaskTailPolyApipelineOpenMem1sprintLongWithCommasslIxFromElementchdir@@GLIBC_2.0readAllWordserrnoWarnhashMustFindValdnaFilterToNlineFileNeedFullNumcmbEndCookieremoveReturnsstarOutoptionIntneedHugeZeroedMemreverseOffsetintSorthashVarLinegetFileNameFromHdrSiglineFileClosestartsWithWordnoWarnAbort__strcpy_chk@@GLIBC_2.3.4bitFindClearaaValhashHistohashTwoColumnFilestrcasecmp@@GLIBC_2.0mustForkverboseVapackDna16twoBitIsSpecbitFindSetaaScoreMatchhashIntValsemiUniqNametoRnafaReadSeqpipelineDumpCmdsdnaUtilOpenneedLargeMemResizeselect@@GLIBC_2.0needLargeMemdlDeleteclosedir@@GLIBC_2.0errnoAbortisReallyStopCodonslCatclose@@GLIBC_2.0countCharsNrTempNamefwrite@@GLIBC_2.0shuffleListpipelineFdmaskHeadPolyTclock1dyStringSubfreeDnaSeqListseqIsLowercopyOpenFilestrstr@@GLIBC_2.0clSeqListtime@@GLIBC_2.0lineFileVaAbortcarefulCheckHeapsetvbuf@@GLIBC_2.0faSomeSpeedReadNextstrncat@@GLIBC_2.0countNonDashtwoBitSpecNewslPairAddhashElFindValsetDefaultMemHandleraaFilterreplaceCharsaaFilteredSizedoubleMedianlineFileSkip__bss_startmalloc@@GLIBC_2.0faReadAalookupCodonreverseComplementslPairFreeValsneedMemfreezpipelineLineFiledyStringAppendN__stack_chk_fail@@GLIBC_2.4slRemoveElfaReadAllSeqlineFileNextCharRowcloneDnaSeqtolowerslineFileNextRowroundingScaleslNameSortCaselineFileMayOpendyStringBumpBufSizedifferentStringNullOkclSeqhashNextValfputc@@GLIBC_2.0differentWorderaseWhiteSpacetwoBitTotalSizelineFileUnexpectedEndmemMatchdnaScore2ntVal5slElementFromIxstdin@@GLIBC_2.0slFreeListslPairFindfaWriteNextdlGetAfterTaillineFileSetMetaDataOutputdlRemoveslRefNewrawKeyInaminoAcidTablefaNextSeqFromMemTextRawdnaOrAaFilteredSizewhichSeqInfaFastReadNextfirstWordInLinememmove@@GLIBC_2.0hashIntSumstringArrayIx__ctype_tolower_loc@@GLIBC_2.3carefulTotalAllocatedstrcat@@GLIBC_2.0ntValhashElFreeListtwoBitSeqSizeverboseDotlastCharlineFileReusegetcwd@@GLIBC_2.0__divdi3pipelineWaitdlValInListslNameNewN_endstdout@@GLIBC_2.0nextPowerOfFourverboseSetLogFileintMedianaddSuffixtwoBitReadSeqFragptToIntfileExistslistDirXpushCarefulMemHandlerdlPopHeaddlAddValHeadslIntCmpRevlistDirfreeDnaSeqfork@@GLIBC_2.0twoBitParseRangetwoBitLoadAllsetMaxAlloc__fxstat64@@GLIBC_2.2twoBitIsFileOrRangereverseIntshashNameIntFiletwoBitSeqNamesuglyfBreakhashAddbitNottcsetattr@@GLIBC_2.0readInGulpvaErrAbortsafencatfaReadAllDnacmbAllocedListslNameListFromStringneedHugeMemResizerand@@GLIBC_2.0stringBetweenoptionFloatusagesizetToPtoptionHashstrspn@@GLIBC_2.0sscanf@@GLIBC_2.0faMixedSpeedReadNextfaReadDnadnaFilter__sprintf_chk@@GLIBC_2.3.4digitsBaseTwodlListResetpushWarnAbortchopByChar__snprintf_chk@@GLIBC_2.3.4_IO_putc@@GLIBC_2.0aaCharsverboseLevelupperToNlineFileDecompresswriteStringdlAddValBeforefirstWordInFilewriteGulpfreeHashAndValslmCleanuppipe@@GLIBC_2.0vasafefslIntNewhashStorefread@@GLIBC_2.0refOnListcrLfChopperpipelineFilecommaSepToSlNameshasWhiteSpacehashToRaStringchopPrefixoptionValcountLeadingCharsstringToSlNames_edataslNameCloneListreverseStringsparseQuotedStringfreeDyStringslDoubleMediansetCurrentDirtwoBitSpecNewFilehashFreeWithValsstrcspn@@GLIBC_2.0lookupMitoCodonprintLongWithCommastrueFalseStringheadPolyTSizeLoosecarefulCloseWarnoptionDoublelmCloneMemlineFileSlurpHttpBodyseqIsDnaskipLeadingSpacesdlAddValAfterfaToProteinferror@@GLIBC_2.0faWritehashAddIntlseek64@@GLIBC_2.1slNameSortstrcmp@@GLIBC_2.0dlAddValTailmemTrackerStartdnaSeqHashdlAddBeforelineFileNextRowTabwarnreadAllLinesfreeMemexit@@GLIBC_2.0readBits64twoBitIsFilecountCharspipelineOpentwoBitToFavalToNtmysqlHosthashTraverseValsgetUserlineFileAttachslCountneedMoreMemvalToAaescCopyslNameLoadRealfaNextSeqFromMemTextlineFileNeedNexthashFromSlNameListdnaOrAaScoreMatchcharSepToSlNamesdlAddHeadhashFirst__i686.get_pc_thunk.bxisDnalineFileSkipToLineStartingWithsafencpybitsInByteInitneedLargeZeroedMemResizefaToDnamain_initlastWordInLinefaSeqListFromMemTextskipNumerictwoBitOutNBedsverboseDotsEnabledgeteuid@@GLIBC_2.0