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Q,3t e S S ~4% P ,S,.P.3S ) \i \ \ T R T $ R$ = Y= S TS R  R ( U( 6 R6 > rH \ \ T R Y R TR'T',R,3\@USlUlSUS$U$4S4LULS~US~U#S#U@TVlTlTVTV$T$4T4LTLV~TV~T#T#TSWUUS$U4LULS~US~U#U]]L]~]~PQ_i_#__i]uPi.0.EPPP0uQia0aQ#%0dQ Q0?~z~Y~~#~ ~~p~z~Z~~#~ ~~I~P~#~ ~~uwPw#w wwu0~ 2$ $ &#1& $ &"~"~"+~ 2$ $ &p1& $ &"~"~"0~ 2$ $ &#1& $ &"~"~"#0~ 2$ $ &#1& $ &"~"~" 0~ 2$ $ &#1& $ &"~"~"0~ 2$ $ &#1& $ &"~"~"u0 2$ $ &#1& $ &"""+ 2$ $ &p1& $ &"""0 2$ $ &#1& $ &"""#0 2$ $ &#1& $ &""" 0 2$ $ &#1& $ &"""0 2$ $ &#1& $ &"""u ~ 2$ $ &~"~" ~ 2$ $ &~"~"# ~ 2$ $ &~"~"  ~ 2$ $ &~"~" ~ 2$ $ &~"~"u  2$ $ &""  2$ $ &""#  2$ $ &""   2$ $ &""  2$ $ &""~P\\P ss`cPcTn~P~`_EVEi__V_\w];];\]#\\wwP~~o0&_0_TPTtTQQ/NP4FPU_TUTr_rUT~TTTr~rTQ~TQTr~rQR]TRTr]rRPTrPclP(BPr{PxP P1QPrSSS ~~$BSlSr___$B_l_] ]~~$1]l]%/P/<QB^^<^^BW]]<]2]]B0PPP0B909WQ0QQ2Q0SWYWW~~<~2~~SWZWW~~<~2~~`dPdW~~<~2~~jnPnW~~<~2~~+~ 2$ $ &p1& $ &""~"W0~ 2$ $ &#1& $ &""~"0~ 2$ $ &#1& $ &""~"<0~ 2$ $ &#1& $ &""~"20~ 2$ $ &#1& $ &""~"0~ 2$ $ &#1& $ &""~"(} 2$ $ &p1& $ &"} "}("W0 2$ $ &#1& $ &"""0 2$ $ &#1& $ &"""<0 2$ $ &#1& $ &"""20 2$ $ &#1& $ &"""0 2$ $ &#1& $ &"""W ~ 2$ $ &"~" ~ 2$ $ &"~"< ~ 2$ $ &"~"2 ~ 2$ $ &"~" ~ 2$ $ &"~"} 2$ $ &} "}("W  2$ $ &""  2$ $ &""<  2$ $ &""2  2$ $ &""  2$ $ &""P\PPmVVmPFIPIjQjrPr}(~#(S~~l|P|}(<~F^$]$B^]^l^<^r~^^V^V<VVrj~~dgPg`~`1~l~U0__l0djQjrPlxPxTtTjrQlQ%DP P. 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S   V . ; H "U Xe u   ]  J /  c C PO /[ g s *  0 V _ ~ x E /i %t     \ $ 0 @< H T f` l      E ;' 3 E> I ;T \  y [   ;  9 T n /v    0     > ` S `  n + F  O 0U d m Sv  ~        % 9& ;R \ {  I  1            ]      K (  1 9 H  M V c ] @j  p py      A *  M '  = Y %^  h <m x   ; ~  @ P @      ` p +% * p3 < dA N W r` e  u ~ MK `  `   R  u   0  i ( =Tr, >   l      =$ 1 6 @ N S O] b m ww | P w   E A6 YA ^L BW b m   @ q   p \" |# p $ " / 8$8@ 0O $X 8$] 0f $o ;%x % _& & w' ' ) ,+ 6, @- e-1Ic~ - -   `   . ~.  / /! /* .03o; J 0O X 0_z/ @ 31 G%=Jq` h E i1  1   W2  2) E3.0N 3Wh_ po 3x 4h  /5  5  @ 5h  G6 5  6  '7 7 K8' 80 c99 9B ;K =T $>] ]?f ?oWxXe_im ?% ?+8I Vi xF   L@ 'A @  A fB B CX p  zC p  C1  C%g&%   4D%6`Lc|Rg  E jD! , .E1 < fEA /L E\ wFj (Gz !H  lH         q" (- 3 lK vf |   X   o - M c I~ m   ! 5  l 8@.symtab.strtab.shstrtab.rela.text.data.bss.rodata.str1.8.rodata.str1.1.rodata.rodata.cst8.rodata.cst16.rela.debug_info.debug_abbrev.debug_loc.rela.debug_aranges.debug_ranges.rela.debug_line.debug_str.comment.note.GNU-stack.rela.eh_frame @!@&","12"@2"O#0W@#d`#wp#r@ضX/ mAF I0@00MP @`0vZ0Ц.H@xH ȭEextract.o/ 1533114431 31235948931 100660 120072 ` ELF>@@f(HT$T$$\$H\f(Df.ATUSHHP'$x'D$p'C<HQ EDSDKHDD$DHD$HD$C DD$@$D$H+DcCD$PC H []A\DRE9uDL$HDJEHQ DHDD$HD$HD$D$PC DD$@$ff.LAHcvA@AH AAHHI@(E@AEAHcA AMcL401;w|1DɃ<At<!<!@SH1H|$@uMt$XHمudT$\urD$`u[D[*Hپt$XHمt[[f.HH HH 7HfAW1E1AVE1AUATUHSHhHL$L$LD$0D$4D$8D$< D$@D$DD$TD$PD$LD$dD$`D$hHD$pD$HHDŽ$HDŽ$HDŽ$HDŽ$HDŽ$D$xD$|DŽ$HLD$XD$\DŽ$HHDŽ$P@BDŽ$HE1Hv($H HH 71Hh[]A\A]A^A_fDD$xkH=1 D$LIH -D$|H= 1D$\@H= 1D$X@H= 1D$H@H= 1$HfDŽ$xAmDH=1 HH$PDH *H=1D$pH= 1D$h@H=LH=LH=LH=1Lbf.D$dKD$`;H=LH=LH=LH=1Lf.D$PD$TD$DD$8{D$4kD$0[1@HH$4@H= 1D$<@H= 1D$@@H=I@DŽ$HH$@H=¾1H HH 7+ T$@GT$<[D$xD$|$L$d$4փt$` & , D$0D$4D$8 HcHTH|H$H$HH$v HcHHtHH$HH$ Mp L$xLT$|&$2D$d$HxLHIľ1H$LHH$HHPH$HHPMm D$0$D$xL Dl$|E $ \$d L1H$LHH$HH7 D\$dE/Hٺ-DL$4ED$E|$xL5t$|L $e D$dE L1H$LHCH$HXH D$d Hٺ-D$8$D$xLDl$|E$\$dL1H$LHCH$HXH D\$dEHٺ-H$ H$H$HT$ Ht$HHH$H)H4$HxIHHH4$LHBD-HHT$~T$ HK9sHH$H2DHHH$H$11D$HIcEIH~ZHL$01HH$H9څ~)L1fH}1H9$HLH5H4H$D$E'DD$0Et$t$4t$T$8t$jH$LH$HtLH$1H hHxIGH=1D$@H=1D$<HxI1H$H8HcH=HT1Hc1H|HcBHtH$HH$H (XHxI,$DL$`LHDl$xl$|$1DL$ DL$ EtHٺEHsD$EMY$DL$`LHDl$xl$|$1DL$ DL$ EtHٺEH$$DL$`LHDl$xl$|$1DL$ DL$ EtHٺEHD$EHxIkH$H8hH$HxH 7H =H &H$HxHxIH EH LH HH 7DHcH|HI.HHtH=L1CL1L1$H$H=1L1SL1?L1+L1H p5L1vH JL1=L1)L1L1L1** +H 3HH$H*H QHH Q#H QH$H$H$HHcH=HT1^HTH=1<ofcmd   FRhv%s %i %i %i %u %u %s %i %i %f %s %i %i %i %s %i %c %u %u C%s %s rbextract.clastCpGlastCHG merged methylation fractions" methylation counts" methylation levels" Invalid option '%c' hvq:p:r:l:o:D:f:c:m:d:F:R:@:config.output_fpoprefwriting to prefix:'%s' %s.cytosine_report.txtwoname%s_CpG.meth.bedGraph%s_CpG.counts.bedGraph%s_CpG.logit.bedGraph%s_CpG.methylKit%s_CpG.bedGraphCpG%s_CHG.meth.bedGraph%s_CHG.counts.bedGraph%s_CHG.logit.bedGraph%s_CHG.methylKit%s_CHG.bedGraphCHG%s_CHH.meth.bedGraph%s_CHH.counts.bedGraph%s_CHH.logit.bedGraph%s_CHH.methylKit%s_CHH.bedGraphCHHfractioncountslogitminDepthnoCpGkeepDupeskeepSingletonkeepDiscordantOTOBCTOTCTOBmergeContextmethylKitnOTnOBnCTOTnCTOBminOppositeDepthmaxVariantFracchunkSizekeepStrandcytosine_reportignoreFlagsrequireFlagshelpversionCAACACCAGCATCANCCACCCCCGCCTCCNCGACGCCGGCGTCGNCTACTCCTGCTTCTNCNACNCCNGCNTCNNfoobar%s.%i %s %i %c %i %6.2f %6.2f Couldn't allocate space for the kstring_t structures in extractCalls()! Couldn't open the index for %s! Couldn't open %s for reading! Couldn't load the index for %s Couldn't allocate space for the data structure in extractCalls()! Couldn't allocate space for the plp structure in extractCalls()! faidx_fetch_seq returned %i while trying to fetch the sequence for tid %s:%u-%u! Note that the output will be truncated! track type="bedGraph" description="%s %s logit transformed methylation fractions" Usage: MethylDackel extract [OPTIONS] Options: -q INT Minimum MAPQ threshold to include an alignment (default 10) -p INT Minimum Phred threshold to include a base (default 5). This must be >0. -D INT Maximum per-base depth (default 2000) -d INT Minimum per-base depth for reporting output. If you use --mergeContext, this then applies to the merged CpG/CHG. (default 1) -r STR Region string in which to extract methylation -l FILE A BED file listing regions for inclusion. --keepStrand If a BED file is specified, then this option will cause the strand column (column 6) to be utilized, if present. Thus, if a region has a '+' in this column, then only metrics from the top strand will be output. Note that the -r option can be used to limit the regions of -l. -@ nThreads The number of threads to use, the default 1 --chunkSize INT The size of the genome processed by a single thread at a time. The default is 1000000 bases. This value MUST be at least 1. --mergeContext Merge per-Cytosine metrics from CpG and CHG contexts into per-CPG or per-CHG metrics. -o, --opref STR Output filename prefix. CpG/CHG/CHH context metrics will be output to STR_CpG.bedGraph and so on. --keepDupes By default, any alignment marked as a duplicate is ignored. This option causes them to be incorporated. --keepSingleton By default, if only one read in a pair aligns (a singleton) then it's ignored. --keepDiscordant By default, paired-end alignments with the properly-paired bit unset in the FLAG field are ignored. Note that the definition of concordant and discordant is based on your aligner settings. -F, --ignoreFlags By deault, any alignment marked as secondary (bit 0x100), failing QC (bit 0x200), a PCR/optical duplicate (0x400) or supplemental (0x800) is ignored. This equates to a value of 0xF00 or 3840 in decimal. If you would like to change that, you can specify a new value here. ignored. Specifying this causes them to be included. -R, --requireFlags Require each alignment to have all bits in this value present, or else the alignment is ignored. This is equivalent to the -f option in samtools. The default is 0, which includes all alignments. --noCpG Do not output CpG context methylation metrics --CHG Output CHG context methylation metrics --CHH Output CHH context methylation metrics --fraction Extract fractional methylation (only) at each position. This produces a file with a .meth.bedGraph extension. --counts Extract base counts (only) at each position. This produces a file with a .counts.bedGraph extension. --logit Extract logit(M/(M+U)) (only) at each position. This produces a file with a .logit.bedGraph extension. --minOppositeDepth If you would like to exclude sites that likely contain SNPs, then specifying a value greater than 0 here will indicate the minimum depth required on the strand opposite of a C to look for A/T/C bases. The fraction of these necessary to exclude a position from methylation extraction is specified by the --maxVariantFrac parameter. The default is 0, which means that no positions will be excluded. Note that the -p and -q apply here as well. Note further that if you use --mergeContext that a merged site will be excluded if either of its individual Cs would be excluded. --maxVariantFrac The maximum fraction of A/T/C base calls on the strand opposite of a C to allow before a position is declared a variant (thereby being excluded from output). The default is 0.0. See also --minOppositeDepth. --methylKit Output in the format required by methylKit. Note that this is incompatible with --mergeContext, --fraction and --counts. --cytosine_report A per-base exhaustive report comparable to that produced with the same option in Bismark's methylation extractor. The output is a tab-separated file with the following columns: chromosome, position (1-based), strand, number of alignments supporting methylation, number of alignments supporting unmethylation, CG/CHG/CHH, trinucleotide context. This is not compatible with --fraction, --counts, --methylKit, or --mergeContext. The produces a single file with a .cytosine_report.txt extension. Note that even bases with no coverage will be included in the output. --OT INT,INT,INT,INT Inclusion bounds for methylation calls from reads/pairs originating from the original top strand. Suggested values can be obtained from the MBias program. Each integer represents a 1-based position on a read. For example --OT A,B,C,D translates to, "Include calls at positions from A through B on read #1 and C through D on read #2". If a 0 is used a any position then that is translated to mean start/end of the alignment, as appropriate. For example, --OT 5,0,0,0 would include all but the first 4 bases on read #1. Users are strongly advised to consult a methylation bias plot, for example by using the MBias program. --OB INT,INT,INT,INT --CTOT INT,INT,INT,INT --CTOB INT,INT,INT,INT As with --OT, but for the original bottom, complementary to the original top, and complementary to the original bottom strands, respectively. --nOT INT,INT,INT,INT Like --OT, but always exclude INT bases from a given end from inclusion,regardless of the length of an alignment. This is useful in cases where reads may have already been trimmed to different lengths, but still none-the-less contain a certain length bias at one or more ends. --nOB INT,INT,INT,INT --nCTOT INT,INT,INT,INT --nCTOB INT,INT,INT,INT As with --nOT, but for the original bottom, complementary to the original top, and complementary to the original bottom strands, respectively. --version Print version and then quit. Note that --fraction, --counts, and --logit are mutually exclusive! Error, the minimum depth must be at least 1! Error: The chunk size must be at least 1! You must supply a reference genome in fasta format and an input BAM file!!! -p %i is invalid. resetting to 1, which is the lowest possible value. -q %i is invalid. Resetting to 0, which is the lowest possible value. More than one of --fraction, --counts, --methylKit, --cytosine_report and --logit were specified. These are mutually exclusive. --mergeContext and --methylKit are mutually exclusive. --mergeContext and --cytosine_report are mutually exclusive. You may specify AT MOST one of -c/--counts, -f/--fraction, or -m/--logit. You haven't specified any metrics to output! Either don't use the --noCpG option or specify --CHG and/or --CHH. Couldn't load the index for %s, will attempt to build it. Couldn't build the index for %s! File corrupted? Still couldn't load the index, quiting. Couldn't open the output CpG metrics file for writing! Insufficient permissions? chrBase chr base strand coverage freqC freqT Couldn't open the output CHG metrics file for writing! Insufficient permissions? Couldn't open the output CHH metrics file for writing! Insufficient permissions? Could not parse the specified region! Could not allocate temporary space for parsing the requested region! %s did not match a known chromosome/contig name! There was an error while reading in your BED file! %lu positions were excluded due to likely being variants. TNGNNNCNNNNNNNNNNNNANNNNNNNNNNNNTNGNNNCNNNNNNNNNNNNAextract_mainextractCalls?Y@F2int$M&;(40|37ԧ%-l.m.s/0 O?      X   sam bam bai   vcf bcf csi gzi tbi bed  _     g gT gT dK e  f? g h iT jKkyz{|}K `tCuuuuu vf wfnx( x0fp~X8 M@DZFuGvGH_J;KK;SnT;mT;aUPLMMMtidN;begN;endN; N;iN;O;O;O; P(offQ0R8V@WN 82a 3[ 3[ 4 5a 6g 7m 8( 9K0B: tid[pos[bin  [ [ [ [~ 8i  ; ;$ i(id0q%BCqbrs[t; t;uuuuauxuovx06;JK~V\ 7l 4 4 <8 ? 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Y ?o?  ?# @ &@  C@ /d@  @ 4@ .@  @ @  A  A  3A NA jA , A wA A  A sB HB  nB B KB  B B  B FC  -C J ?C QC  cC  ~C  C C TC C  C D  #D =D  ]D sD yD D  D " D 5E *E 1E GE  ]E yE d E E E wF  8F SNF K_F 'vF F $F 4 @5 JK1LML}M_M_M_  8P|@0@tp0p.symtab.strtab.shstrtab.rela.text.rela.data.bss.rodata.str1.1.rodata.str1.8.rela.rodata.rodata.cst8.rela.debug_info.debug_abbrev.rela.debug_loc.rela.debug_aranges.debug_ranges.rela.debug_line.debug_str.comment.note.GNU-stack.rela.eh_frame @2@+x-+`2 &@(YX1 762 7E2:#Y^ T@^adsdFn@n\ N@0@p0 @0  0.@  h'DMBias.o/ 1533114431 31235948931 100660 64840 ` ELF>@@AW AVAU ЉAT USH ЉH( ŃILcIH{LH{LHCH{LHCH{ HCLL[HC MLLKMLSMdHBDCD9McJ<D)L$I:I49I ;HLzLvLiL<$LL9Lt$L|$AL9AE H; $AL9D$D t$E!H;T$AH;4$D$D t$E!|$ AE!H;L$AL9AE E!H;T$AH;<$AE EH;t$AH;|$EAEDl$AF4Etunmeth1s->unmeth2s->meth1s->meth2methsmeths[i]rbInvalid option '%c' hvq:p:r:l:D:F:@:noCpGCHGCHHkeepDupeskeepSingletonkeepDiscordanttxtnoSVGnOTnOBnCTOTnCTOBchunkSizekeepStrandignoreFlagsrequireFlagshelpversionCouldn't open the index for %s! Couldn't open %s for reading! Couldn't load the index for %s Couldn't allocate space for the data structure in extractCalls()! Couldn't allocate space for the plp structure in extractCalls()! faidx_fetch_seq returned %i while trying to fetch the sequence for tid %s:%u-%u! Note that the output will be truncated! (meths[strand-1]->unmeth2[(plp[0]+i)->qpos]) < 0xFFFFFFFF(meths[strand-1]->unmeth1[(plp[0]+i)->qpos]) < 0xFFFFFFFF(meths[strand-1]->meth2[(plp[0]+i)->qpos]) < 0xFFFFFFFF(meths[strand-1]->meth1[(plp[0]+i)->qpos]) < 0xFFFFFFFF Usage: MethylDackel mbias [OPTIONS] Options: -q INT Minimum MAPQ threshold to include an alignment (default 10) -p INT Minimum Phred threshold to include a base (default 5). This must be >0. -D INT Maximum per-base depth (default 2000) -r STR Region string in which to extract methylation -l FILE A BED file listing regions for inclusion. --keepStrand If a BED file is specified, then this option will cause the strand column (column 6) to be utilized, if present. Thus, if a region has a '+' in this column, then only metrics from the top strand will be output. Note that the -r option can be used to limit the regions of -l. -@ nThreads The number of threads to use, the default 1 --chunkSize INT The size of the genome processed by a single thread at a time. The default is 1000000 bases. This value MUST be at least 1. --keepDupes By default, any alignment marked as a duplicate is ignored. This option causes them to be incorporated. --keepSingleton By default, if only one read in a pair aligns (a singleton) then it's ignored. --keepDiscordant By default, paired-end alignments with the properly-paired bit unset in the FLAG field are ignored. Note that the definition of concordant and discordant is based on your aligner settings. -F, --ignoreFlags By deault, any alignment marked as secondary (bit 0x100), failing QC (bit 0x200), a PCR/optical duplicate (0x400) or supplemental (0x800) is ignored. This equates to a value of 0xF00 or 3840 in decimal. If you would like to change that, you can specify a new value here. ignored. Specifying this causes them to be included. -R, --requireFlags Require each alignment to have all bits in this value present, or else the alignment is ignored. This is equivalent to the -f option in samtools. The default is 0, which includes all alignments. --txt Output tab separated metrics to the screen. These can be imported into R or another program for manual plotting and analysis. Note that coordinates are 1-based. --noSVG Don't produce the SVG files. This option implies --txt. Note that an output prefix is no longer required with this option. --noCpG Do not output CpG methylation metrics --CHG Output CHG methylation metrics --CHH Output CHH methylation metrics --nOT INT,INT,INT,INT Inclusion bound for methylation calls from reads/pairs originating from the original top strand. Each integer represents a 1-based position from the end of a read. For example "--nOT A,B,C,D" translates to, "Include calls from position A through the Bth read from the end on read #1 and Cth through the Dth from the end base on read #2". In other words "--nOT 5,10,0,0" for a 100 base long read would result in bases 5 through 90 being used. If a 0 is used in any position then that is translated to mean start/end of the alignment, as appropriate. For example, --nOT 5,0,0,0 would include all but the first 4 bases on read #1. --nOB INT,INT,INT,INT --nCTOT INT,INT,INT,INT --nCTOB INT,INT,INT,INT As with --nOT, but for the original bottom, complementary to the original top, and complementary to the original bottom strands, respectively. --version Print version and the quit Error: The chunk size must be at least 1! You must supply a reference genome in fasta format, an input BAM file, and an output prefix!!! -p %i is invalid. resetting to 1, which is the lowest possible value. -q %i is invalid. Resetting to 0, which is the lowest possible value. You haven't specified any metrics to output! Either don't use the --noCpG option or specify --CHG and/or --CHH. Couldn't load the index for %s, will attempt to build it. Couldn't build the index for %s! File corrupted? Still couldn't load the index, quiting. Could not parse the specified region! Could not allocate temporary space for parsing the requested region! %s did not match a known chromosome/contig name! There was an error while reading in your BED file! mbias_mainextractMBiasgrowStrandMeth)u$8&Qint(c0u37Ԡ%-l.m.s/0 O8      X   sam bam bai   vcf bcf csi gzi tbi bed  _     g g? g? dD e f8 g h i? jDkyz{|}D `t<uuuuu vX wfnx( x0fp~Q8 F@DSFxuGvGHXJQDDQSnTQmTQaUPLMMMtidNQbegNQendNQ NQiNQOQOQOQ P(offQ0R8V@xWG 82Z 3F 3F 4 5Z 6` 7f 8( 9D0-: tidFposFbin  F F F Fw 8b  Q Q$ b(id0jB<q br sFtQ tQuuuuauxuhvx)/QCD ~OU7e i k nQ ovalpQ c c 0 P Q     ( 0 8 @ H P X  `  h Qp Qt x | 8     & /D 0D 1D 2D 3 5Q 7 `    Qg  `   <8 ?  A  Bc 7 E  K? M? N?   O ( \ ^Q _ `Q b fQ h? i? jE ( Z  |P  }  ~c '   !  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Usage: MethylDackel mergeContext [OPTIONS] This program will merge single Cytosine methylation metrics into per-CpG/CHG metrics. The input file must be coordinate sorted but is not required to contain only a single sequence context, though not doing so may result in an unsorted result. ref.fa Reference genome in fasta format. This must be indexed with samtools faidx input An input file such as that produced by MethylDackel extract. Specifying - allows reading from a pipe. Options: -o STR Output file name [stdout] --version Printer version and quit You must supply a reference genome in fasta format and an input bedGraph files Couldn't open the index for %s! 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