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U/4: ;I 04: ;I ,1: ; I ,2 : ; 3: ; I ,441 ,5&I : ; 6.: ; ' I 7$ > 8I9!I/ :4I: ;  ;!I/<4I? : ;  = I: ; 8 UWU`pUpS 1U17U7S 1T1T^U^^TSSQVVRRUUTTVQQV=V=VY[ R[ ePeP P P, " Q" Q QQ3Q3XQX}Q}QQ Q Q P PUUTTXRQR&Q&0R03^3^QRQRSSU0SvP0^0BUBSU%$S0$H$UH$%S0$E$TE$Y$VY$%V"kh_resize_refbam_char2flag_table+isalphakh_init_refalloc_dataLisasciiks_destroykh_put_refks_getuntil__inline_strncpy_chkbam_aux_type2sizesam_read1isdigittoupperks_initsam_open;sam_header_read4bam_nt16_tablesam_closekh_destroy_refks_getuntil2 __inline_memset_chk@__istypehash2headerks_getcsam_header_parselparse_error__bam_get_lineslisspaceUbam_nt16_rev_table__ac_X31_hash_stringsam_header_read2bam_reg2binf__inline_strcpy_chk__ac_prime_listappend_text__inline_memcpy_chk__isctype>"__tamFile_t__kstring_tg__kstream_tks_destroyks_init__ac_X31_hash_stringks_getuntil2isspace__istypealloc_dataisdigit__isctypeisalphaisasciitoupperparse_errorbam_reg2binbam_aux_type2sizekh_init_refkh_put_refks_getchash2headerkh_destroy_refQ^  7==Zy#o!FFk.o(FFkFkkt  0G"p""          @ p= ף??-rbParse error at line %lld: %s *[sam_read1] missing header? Abort! [sam_read1] reference '%s' is recognized as '*'. invalid CIGAR characterinvalid CIGAR operationunmatched CIGAR operationParse warning at line %lld: mapped sequence without CIGAR =Line %ld, sequence length %i vs %i from CIGAR CIGAR and sequence length are inconsistentsequence and quality are inconsistentmissing colon in auxiliary dataParse warning at line %lld: integer %lld is out of range.length of the hex string not eveninvalid hex charactertoo few values in aux type Bunrecognized array typeunrecognized typerealloc failed to alloc %ld bytes append_text FIXME: %ld>=%ld, x=%ld,y=%ld SQSNLNr[sam_header_read2] duplicated sequence name: %s [sam_header_read2] %d sequences loaded. =ACMGRSVTWYHKDBN 5a 0`   0 ` Y0`zRx 4W 4T  4  4  4| 44C 4l0 4  45  4   /Users/macleand/bioruby-samtools/ext/samtools-0.1.18//usr/include/secure/usr/includebam_import.c_string.hkhash.hctype.hbam.h      |  | ( 0 I R `m p z      |  |     | 1 1 7 7 7   6 `   } g            0  ~  ~ + :~ ? 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" 3" G"t p" |" " " " " # 0# <#P D# D# N# `# r# # # # # # # # # # # # $ 0$L E$ H$ H$ H$ R$ $ $B $R $B $ $S $ $@ $  %_ %  % -% ]%t n% % % % % % %ks_destroy"M$ks_init p$__ac_X31_hash_stringF ks_getuntil2%.isspace1__istype8 alloc_data@ N X e  s0 I ,a y !!isdigitJ e , N  : A o __isctypeQ;  , s  V A isalphaZ isasciia5  toupperh  Fparse_erroro   F  ( MrIbbam_reg2binz ! bam_aux_type2size1kh_init_refgkh_put_refd ks_getcp"hash2header<#kh_destroy_ref#%-%W-%F-y%S-%J-%J- %L-%J-$J-$-$P-$F-$F-$N-$t$M-m$f$H-^$;=S$V-K$ $J-$J-#J-#J-#E-j#F-X#F-=#D-,#I-%# #:= #J-#J-"L-"J-"J-"O-H"- "I-"!:=G!V-B - ?- -X--F-P-{F-hF-JN-B9M-2+H-#;=V-E------p-ED-J- ?-F-T-J-X-F-lT-d]OU-J-J-=-I-:==-I-:=Z-LS- :=:=I-:=B-uG-kK-\$-[-Q-gS-<-\-J\-\-\-Z\-\-kS-S-n:=b[I:==6$:=S->-zS- :=I-:=F@-1S-S-:= |:=hY-~V-vU-*8-S-;B-Y-V-  - ?- 7=z -\ ?-P 7=0 - C- V-  - I-  := A-   :=` <-P \-, %  := S-B =-= I-6 /  := 9- 7= -A ?-5 7= -?-7=-I-:=V-ygC-R-(\--Q-S->Y--gF-Q-S-@9-9-UO-"7=J-S-S-S-S-R-P-  qMP-F-F-F-N-M-H-;={V-sNJ-BJ-9J-,L-$J-J- d,Pr M  ZRD/yRJ um5  v`:2ph>;3ogVN>6&  ~ n f V N = 5             S K            x c [ K C . &             x _ W B : -         v n [ H @ 0 (  mW~o_P?7 e]TA~iRJ0( umbZOG,$woTLA9 vnc[PH=5*"umRJ?7,$qi^V;3(  sk`XME*"umbZOG,$tlQI>6h`XP80( h`XPH@80xpXPH@80!'^&2^10^/p.^p-8%^86^5$^#^X4^X3 ,^ +{ocWI=1% th\PD8, vgYMA5)vg[O@4(}qeYMA5)sg[OC7+ui]QE9-! ym^OC7+ym^RF:+}nbTC5){ocWK?3'|m^RF7( |maUF:."th\PD8,           | p d U F : .              } q e Y M A 3 '              | p d X L @ 4 &             ~ r a P D 8 ,             | p a U I : .    vj^RF:.seTF5)xl[OC7+wk]QE4(znbVJ>2&|k]L>2&th\PD8, ui]QC7+tX; fZA({ocWK?3'dXL3'XX [;XhXXXXXX#YY!Y*Y3Z<2ZEHZN@XV(Y_XYheZq}ZzZZZZZZZ([Q[\\\0]0$^ V  X/ U \kIh]0^]r]`.P\;\q&-F? P\7 T?HX`h}%bL_sam_close_free_gzclose_sam_open_strcmp___stdinp_fileno_gzdopen_gzopen_calloc_malloc_memset_realloc__DefaultRuneLocale_gzread___maskrune_memcpy_sam_read1_strlen_strtol_bam_char2flag_table_bam_get_tid___stderrp_fprintf_atoi_abort___toupper_bam_calend_bam_cigar2qlen___bzero_bam_nt16_table_atoll_atof_strtod_fwrite_exit_strncpy_sam_header_parse_sam_header_parse2_sam_header2list_strdup_sam_header_read_bam_header_init_bam_init_header_hash_sam_header_read2___bam_get_lines_strcpy_bam_nt16_rev_table_sam_close.eh_sam_open.eh_sam_read1.eh_sam_header_parse.eh_sam_header_read.eh_sam_header_read2.eh___bam_get_lines.ehL_.strL_.str1_kh_resize_ref___ac_prime_list_ks_getuntilL_.str3L_.str5L_.str2L_.str6L_.str7L_.str8L_.str9L_.str10L_.str13L_.str14L_.str15L_.str16L_.str17L_.str18L_.str4L_.str11L_.str12L_.str19L_.str20_append_textL_.str21L_.str22L_.str23L_.str24L_.str25L_.str26L_.str27L_.str28L_.str29EH_frame0_kh_resize_ref.eh_ks_getuntil.eh_append_text.eh #1/12 1320240673 37557 39398 100644 18860 ` sam.o H..__text__TEXT4h__debug_frame__DWARF|x7__debug_info__DWARF$ L84__debug_abbrev__DWARFpG@!__debug_aranges__DWARF#__debug_macinfo__DWARF#__debug_loc__DWARF}#9^__debug_pubnames__DWARF4"(__debug_pubtypes__DWARF #(__debug_str__DWARF2#,)__debug_ranges__DWARF^#.)__data__DATA^#.)__cstring__TEXT`#E0)__eh_frame__TEXT$x*< h__debug_line__DWARF8&,=__debug_inlined__DWARFU.e%4 B$BFF P ,UHAWAVATSH0Iƹ LHHIF(IFIF I~0HǾIF@Hs@IV0HIc>IFIc>IFA>~2E1fHCBINBHCJL[A\A^A_]UHAVSHu 1HILHxHHLH5HHHuLu HH8H50LHgH8| HHH="L:HHH=(H1[A^]fDUHAWAVSHHtUHuKuVH{ILIHsLHs LDH[A^A_]H{H[A^A_]fDUHHttHuHGHwH]]HH]DUHAWAVAUATSHHIAI8ILHHHDMu=LHA$t)tI|$LI|$It$Ly1HHMtI}0L1H[A\A]A^A_]DfDUHSHHtDHH{Htt H{H{tHH[]H[]UHAWAVAUATSHHIIIľrLHE,$DA$bLHtiAE,$H5LtH5LHH;H5ID$HHID$LID$HHIMt$A HHID$HHM~@MEn0H{0B/  ȉ  ȉ  ‰ Љ ‰ 9|HC@H{@HcHC@H{0HMcLLLk0Lk0L{@C/LH;HH H=&H;HH;H50twLH^HID$bLH1HL@@ rHH@2@uH AuоuLHDÅEwy00EEA $H5LtHuLL5I>HuՉID$HIt$HkH5LtH5L HHID$HAXLHtA $xLHA$tA$hLH0HID$H@0HC0ID$H@@HC@HHC0HC@IL$Mt$IV0I~@AuI~vE1L-fDIFMvJC I|$0LIMt$E9>19t-L5A>~ L5IH=KHLH[A\A]A^A_]L1x 4 0 0  $p; 4  ,Y 4  H4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.1.00)sam.c/Users/macleand/bioruby-samtools/ext/samtools-0.1.18/intint32_t#charunsigned intuint32_t7long unsigned intsize_tHWn_targetsX#target_nameY#target_lenZ#dict[#hash[# rg2lib[#(l_text\#0n_text\#8text]#@bam_header_tYbam_header_dupbam_header_dup V h0   h ^ i  __inline_memcpy_chk<__dest;__src;__len;<samfaipathsamfaipathV fn_refb6  fn_listSx +P  x__inline_strcpy_chk]__dest\__src\b__inline_strcat_chk__dest__srcbMsamwritesamwritejV fpM l b j L s^ l_@samreadsamread~pV fp}M b}!yssampileupsampileupuV fpM j mask func func_data2 u buf3SretbM :samclosesamclosetV fpsM {__tamFile_ttamFileshort intint16_tlong long intint64_t(5"knetFile_stype#fd#offset#host#port#ctrl_fd# pasv_ip%#$pasv_port#4max_response#8no_reconnect#<is_ready#@response#Hretr#Psize_cmd#Xseek_offset #`file_size!#hpath$#phttp_host$#x5knetFile$unsigned char__sbuf`_basea#_sizeb#"fpos_t`R**8 Zbj__sFILEX"" __sFILE_p#_r#_w# _flags#_file#_bf#_lbfsize#(_cookie#0_close#8_read"#@_seekR#H_write#P_ub#X_extra#h_ur#p_ubuf#t_nbuf#w_lb#x_blksize#_offset*#FILE` !I )fpr*#fpw +# X$file_descriptor%#open_mode&#owned_file'#compress_level'#x$ ,#uncompressed_block_size0#compressed_block_size1#uncompressed_block2# compressed_block3#(block_address4#0block_length5#8block_offset6#<cache_size7#@errorb8#Hcache9#PI BGZF  bamFileW! tamr#bam #tamw #< type#x #header# samfile_t<  samopensamopen(M V fn'b mode'b aux'0 fp)M "- textheader8 ; _# y# "y p& compress_levelFSbmodeE;iF  altYSiX$append_header_texttextheaderlen%yx K__inline_strncpy_chk__dest__srcb__len tid#pos#&bin#&qual#&l_qname#&flag# &n_cigar# l_qseq#mtid#mpos#isize#Kbam1_core_tuint8_t-!8core#l_aux# data_len#$m_data#(data0#08bam1_t'^(b#(qpos#(indel# (level#)is_del#)is_head#)is_tail#)is_refskip#)aux#bam_pileup1_t^t|bam_pileup_f#__bam_plp_tbam_plp_t'#(iter$#(func%#(data&#bam_plbuf_t1*"% R $>  I: ; I : ;  : ;  : ;  I: ; 8 .@: ; ' I? @ : ; I  4: ; I , 4: ; I , .: ; ' I: ; I1X Y 1 ,.: ; ' I  .@: ; ' I? @  4: ; I1X Y .@: ; ' ? @ < I: ;$ > I!I/  : ; I' I &I : ; ! : ; " #41$.: ; ' % & I: ; 8 ' : ;( I: ;8 ) I: ; 8 *IUSUUUjUTTjTptUtUptTtwTwQUu\T_uTQ^uURSuTUUU__T^QSS$R$+P+2R29P9;R;RAHPHOQOVPV]Q]_P_PLbam_header_dupsampileupx__inline_strcat_chkMsamreadU samopen append_header_text<__inline_strcpy_chkssamclose__inline_strncpy_chkY__inline_memcpy_chksamwritesamfaipathL__inline_strcat_chksamreadappend_header_text.fai[samfaipath] fail to read file %s. [samfaipath] build FASTA index... [samfaipath] fail to build FASTA index. -r[samopen] no @SQ lines in the header. [samopen] SAM header is present: %d sequences. w[samopen] inconsistent number of target sequences. 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I v00010E]_L?Cp= ף??bam_iter_readbam_index.citer->curr_off == iter->off[iter->i].vftp://http://r[download_from_remote] fail to open remote file. wb[download_from_remote] fail to create file in the working directory. BAI[bam_index_load] wrong magic number. .bairbbam[bam_index_load] attempting to download the remote index file. [bam_index_load] fail to load BAM index. Usage: samtools idxstats [%s] fail to open BAM. bam_idxstats[%s] fail to load the index. %s %d %llu %llu 0 0* 0 0 %llu [bam_index_core] the alignment is not sorted (%s): %d-th chr > %d-th chr [bam_index_core] the alignment is not sorted (%s): %u > %u in %d-th chr [bam_index_core] bug in BGZF/RAZF: %llx < %llx [bam_index_core] the alignment is not sorted: reads without coordinates prior to reads with coordinates. [bam_index_core] truncated file? Continue anyway. (%d) [bam_index_build2] fail to open the BAM file. [bam_index_build2] fail to index the BAM file. [bam_index_build2] fail to create the index file. 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Continue anyway. resolve_cigar2bam_pileup.ck < c->n_cigars->k < c->n_cigar[%s] unsorted input. Pileup aborts. bam_plp_nextzRx 4 ,T ,  , ,$ 4  4LG  4  ,  4C  4$Z  4\d ," 4  4  44  4l 4R  [ /Users/macleand/bioruby-samtools/ext/samtools-0.1.18//usr/include/securebam_pileup.cbam.h_string.h     -~ 2 5 5s 5# ; _ z z                    $ $ $ ' 0+ 4 4 4d 9 C4 F` F I3 PU T T T W ` n r j              7 F L `K p s }      D         ~  $ 1 I V c k :             |            " , 5 ? B B J P b   |     , A J [ ^~ ^ ` x    i "     ~  ~     ! 8 D G~ G K~ M M U e u    ~          + @ D G G x  F      ~            5 ` e l)   i 5       o    . p >  i  q  {                  ;  A  Q  d  j                      <  F  K  R r U  s %        \       ~   .  ?  W  d t             ~    (   ~     W                ] ! J O{ O~ O O O' i& nk n~ n n n' n p t           Q     ( 0) 0 0k :, F O S [R [ [2 [d )   0  e  B           # % - 6 @ \ f {                & 9 [ ` h {         Bmp_init-mp_allocJ5uz5 ^24w[mp_free NG bam_copy1& mp_destroy/resolve_cigar29^`GG0UUD[gg-$-|&-]$-H&-$-4-4-4- --1--G"-;2-)2-$-$-&-j.-eYRK.-F:3 7-K 7-3-yrh/=a.-\PI4- -4-4-4-4-y4-e -64-$4-4-4-4-4-4-4-3-/=7--7-/=r2-5- /=0-^6-F7-(-=7-"-~2-'"-2-2-2-2-2-2-2-P2-.2-2-p8`,`,|T]UL8l |oUM;$ jbogDO#_W/'Y B :        x        z L D j V N    pY?7*"}u<4zl[SA0(              ~ s k ` X = 5 * "             u m b Z O G , $    wod\A9.& yqVNC;0( {sh`E=2*meZR7/$|tYQF>3+nf[S80%ph]U:2' }rjOG<4wod\QI.&XPH@( xph`H@80( xph`H@80 ^ p^p8^8^%^$^` ^` (!^( '^&^)^(P^P^^^-^,X+^X* #^ "TH<0$ |pdXL@4(th\PD8, |pdXJ>2&|pdUI=1% ~rfZNB6*          | p d X I = 1 %              { o c W K ? 3 '               p d V J > 0 $              w k _ S G ; / #              v j ^ R F : . 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I: ; 8 "I: ;# : ; $I' %I&< ' : ;(.: ; ' I ).: ; ' I@ *.: ; ' I+$ > ,I-!I/ .&I : ; U-U-VTTQQUUTTQQUUUUTTSUUUTTUS`iUiU`iTiT U UU T TV  U UUU UT TQ QT T U U U T T U S U ^ 3 ^ T S 3 SD [ U[ d Vd VD X TX d Vd VD U QU QD U RU a Va VD Q XQ X$U$SU{UTT{SUVTVVmp_freeks_ksmall_node bam_lplbuf_initOks_heapsort_nodemp_destroymp_alloc<ks_heapadjust_nodexks_combsort_node(ks_shuffle_nodemp_initbam_lplbuf_pushbam_lplbuf_resetks_introsort_nodeks_mergesort_nodetview_funcY__inline_memcpy_chkbam_lplbuf_destroy__ks_insertsort_nodeks_heapmake_node2 __bam_lplbuf_t__freenode_t__ks_insertsort_nodemp_freemp_destroymp_initmp_alloc@ D Q Q U U X X [ [ !!$$0E]_L?Cbam_lplbuf_destroybam_lpileup.ctv->mp->cnt == 0tview_funcl == tv->n_prezRx 4 4T 4R  4E 4 44  4l  , 4  4   4D  4|  4{  4   x /Users/macleand/bioruby-samtools/ext/samtools-0.1.18//usr/include/securebam_lpileup.c_string.h "      @ E E   ' 1 U h k                  0 N ` i i            0 k          * @      R  ]  p  }  %  3              o                 3  : ~ _  q  ~        ~            ' ~ '  V  f    j        ~   ~              (  @  D  Q  Q  U  U  U  X  X  [  [  k              T Z   E     K  ! 6 N X }    [             G c c p |         h   / 4 6 : : ? i u }      P J  ! $ $ - 5 P Wf |    '      E     0 l     Y Y Y |   K|mp_freeg: ~ $Wmp_destroy' mp_init%` mp_alloc,w )--f*-;(-,-)&-"-+-;-,-S,-'-,- ,- ,- $-  '- '- '- "-  | u )-_ )-W )-E )- ,- ,- )- #- )- )- %-%   G--)-A*-d,`(TkW@+#YQE=1)y|meNFtlV.&phUM6.zriXP& LDz<4 sk(g_@)QI>6+#vnSK@8 h`UMB: zrg_D<1)|tYQF>#nf[SH@% ph]UJB' rj_W<4)!d\QI.&xpXPH@80^!^ ^H^H ^  ^ ^p^p8^8 ^^^X^X ^    s g [ O C 7 +               u i ] Q C 7 +               s g [ O C 7 +    th\PD8, ui]QE7+wk_SG;/ ~rdXL@4% wk_SG;/# ymaUI=1% }qeYMA5)ui]QE9-! i]QE9 <<<@ <<=P?Z`> > 5? >5I?p@>"`=6=H=r?x>r(=X^? 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VToSo SQ VP P P  P@y^y ^ $ U$ ) U) / U $ T$ ) T) / T4 A UA U4 A TA T T4 A QA Q V b aUVT|V|V Q VR|V|VrVPU U VT T VUUUTTTQQQ[obam_fillmd1_core]bam_cap_mapQbam_prob_realn0 bam_nt16_nt4_tableHkputc} bam_fillmd bam_fillmd1bam_prob_realn_core__inline_memcpy_chkkputwZ toupper[__kstring_tkputctoupper!! 4 A A   \iZ\iD?D@Zd;_@V-?BQZQNM[bam_fillmd1] different NM for read '%s': %d -> %d MD[bam_fillmd1] different MD for read '%s': '%s' -> '%s' RG[bam_fillmd] unrecognized option '-%c' EqreuNhbSC:n:AdbhuUsage: samtools fillmd [-eubrS] Options: -e change identical bases to '=' -u uncompressed BAM output (for piping) -b compressed BAM output -S the input is SAM with header -A modify the quality string -r compute the BQ tag (without -A) or cap baseQ by BAQ (with -A) -E extended BAQ for better sensitivity but lower specificity [bam_fillmd] input SAM does not have header. 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[fai_build_core] different line length in sequence '%s'. %s.fai[fai_build] fail to open the FASTA file %s [fai_build] fail to write FASTA index %s ftp://http://[fai_load] failed to open remote FASTA index %s [fai_load] build FASTA index. [fai_load] fail to open FASTA index. [fai_load] fail to open FASTA file. 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[bam_merge_core] cannot open '%s': %s .bamr[bam_merge_core] fail to open file %s [bam_merge_core] different target sequence name: '%s' != '%s' in file '%s' [bam_merge_core] number of @SQ headers in '%s' differs from number of target sequences [bam_merge_core] @SQ header '%s' in '%s' differs from target sequence [%s] Malformated region string or undefined reference name bam_merge_core-wu[%s] fail to create the output file. RG[bam_merge_core] '%s' is truncated. Continue anyway. [bam_sort_core] fail to open file %s [bam_sort_core] truncated file. Continue anyway. [bam_sort_core] merging from %d files... nom:Usage: samtools sort [-on] [-m ] h:nru1R:fUsage: samtools merge [-nr] [-h inh.sam] [...] Options: -n sort by read names -r attach RG tag (inferred from file names) -u uncompressed BAM output -f overwrite the output BAM if exist -1 compress level 1 -R STR merge file in the specified region STR [all] -h FILE copy the header in FILE to [in1.bam] Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users must provide the correct header with -h, or uses Picard which properly maintains the header dictionary in merging. rb[%s] File '%s' exists. Please apply '-f' to overwrite. Abort. bam_mergezRx 4 4T{  4  4  4a  44  4l  4c  4E 4R  4L 4c  4\  48  4,  4dR  4  4x 4 R  4Dy  4|e  4  4  ,$  4T   0 /Users/macleand/bioruby-samtools/ext/samtools-0.1.18//usr/include/usr/include/securebam_sort.cctype.h_string.h H      ? 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Y? b? n? ? ? ? ? @ @ O@ T@ l@ @ @ @ @ @ @ A A .A WA \A `A pA yA A A A A AP A AL B B B B B  B EB ZB jB mB |B B B Bm B B B B B B~ B B B B B C "C %C# (Cq :C GC `C yC C C C C C D (D AD Di D D D D D E E E' GE OE OE [E E E E E E EUheap_lt c K'7+-isdigitm__isctypebam1_lt " H !a(a*swap_header_targetse8swap_header_text1p9AAo;Ex-E)E(E^=E=Eu-Ez-Ez-E3-TE=HEw-@E'5E--EE-D-D|-DhD~=VD{-GD&=D{-.D%$D{-D$ D{-C#C{-C"C{-C!C{-C C{-CC{-CuC{-fC\C{-MCCCy-6C^=C=C|-BB9-B9-B{-BxB^=fB=[B|-IBa-AB~=BAx-AA^=Ap-Ae-Az-Az-~Az-aAz-XAz-PA3-Az-A-@z-@3-@]-@@s-@-a@s-P@]-B@0@]-%@ @s-?-?-?x-??^=?-?{-t?j?^=Z?n-K?s-?->s->f->q-> >v->_=>r-> v>-n>g>>z->z- >z->p-=p-=j-=z-=z-=z-g=?-U=x-M=A=^=(=z- =z-<l-<o-<b-m<c-]<d-;<<?-;e-;g-;;^=;q-;;v-;`=;;;v-};`=t;\;-P;G;@;v-8;`=,;r- ;;- ;:l-:s-C:h-8:k-$:i-9x-99 9^=9m-9e-V9x-;9- 9 9^=8x-8 8^=8e-F8-8r- 8 7f-7x-7 7^=p7z-g7z-T7p-;7x-47*7^=6-6s-w6-o6[6- 6s-5s-5s-5s-5s-5y5-j5-U5x-D5:5^=35-,5\-"5-4--4z-x4;-g3-23m2-g2m2-1m0-0m0-/m.}----m/-p--o-,g-,z-,z-,x-,,^=,r-,q-,v-,`=,]-x,\,]-O,4,s-&,-,U-+z-t*-c*m(-(m'}-h'/-I'z-2&-"&m%-z%m$-$m4$-$$m#-#mK#=-"}-!-!mZ!?-!?--m -mH--E-mx l L S-)m-amL-m-xm-m-m-mA-wA--m*-m/-O->mH <  5-$m[ -K m -t m - m - my -h m - m--w[=t-;t-z--em -m@}-<l4X$|Dl4Tr/~v{NFjV|t]U;3qXE=%5" M80nf/ia7"nf:2[G3kc<4xp^V-%D<XP!kcLD-%      x o   b Z / '       U M @ 8 /     e K C :     j b ; 3 kcKC+# ]ULzr }u5- U?,$d\=&}rj_W<4)!|aYNF;3~sk`X=5*"umbZ?7,$          w o d \ A 9 . &             y q f ^ S K 0 (             { s h ` E = 2 *             } u Z R G ? 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@ : ; I: ; I  4: ; I ,4: ; I , 4: ; I U  U $ > I!I/4I: ;   : ;  I: ; 8 I: ; 4I? : ;  I : ; !I/ /U/VV+T+V(Q(VV!R!VXSSYVM1kpa_par_defkpa_glocal*g_qual2probkpa_par_alt1gmmrjgmmrs&D\s     o:= 8 #< $@??jTUUU?0.++Zd;_V-???zRx 4 T /Users/macleand/bioruby-samtools/ext/samtools-0.1.18/kprobaln.c ]   ! ( + / / / 1 6 E I I g m m r        5 T v        J ] z                     ( X    & D \ h        * =  h   "  D  X   l  ,           -      " F  N  N  R  X  X         B  e   -    ! s   %      G t   j j   s   O n    , > B r *   ---_ W O-F -     :   [ -O -C -, -J 9 1 - L 6 . -#   J B :  z r T  Y - zg-I-----  ?~hL'vcO'?)w^VbZOG,$d\QI.&h`XP80( h`XPH@(  ^ wk_SG;/# ymaUI=1% }qeYM?3'sg[OC7+wk_SG;/# {ocWK?0$ ymaN)["?"2 ("% " _kpa_glocal_calloc_pow_log_free_kpa_par_def_kpa_par_alt_kpa_glocal.eh_g_qual2probEH_frame0 #1/20 1320240681 37557 39398 100644 10948 ` bam_cat.o H__text__TEXT \J__debug_frame__DWARF  !__debug_info__DWARF ` !__debug_abbrev__DWARFm__debug_aranges__DWARFX__debug_macinfo__DWARFX__debug_loc__DWARFXD""__debug_pubnames__DWARF+C__debug_pubtypes__DWARFn>__debug_str__DWARFP__debug_ranges__DWARFpPT# __data__DATA__cstring__TEXT|__eh_frame__TEXTp@# h__debug_line__DWARF#@__debug_inlined__DWARFR%/( PUHAWAVAUATSHXHHUHu}HHHEH5HtH5HHH8H5HEH}uJHH8H5H0HHHH;E+HX[A\A]A^A_]H}t H}HuHEHLuH]J HH;H5H0HHH;]zH]HuH HH;H5A~r[LH}HEuHEu H}HuAV8IcF<9}Iv H)H}H}HELxE1#HHEL4LHHtLHH L5I>L5LIM5AYEMcHEHǾLLD)LcJt%HEHLJ|-HLXEtHEHǾLAIcDdDeHDHEHHLHMHEH߾LAI~H޺AE&}u E  .@: ; ' I? @ : ; I 4: ; I 4: ; I ,4: ; I , 4: ; I U  : ; .: ; ' I : ; I UI : ; &I : ; I: ;  : ;  I: ; 8 $ > I!I/  : ; I' I< I: ; : ; U>V>VT>V>VQ>V>VRSUU ^TT S? bam_cat&__inline_memcpy_chkomain_cat :Y?7a-w[%s] ERROR: fail to open output file '%s'. bam_catr[%s] ERROR: fail to open file '%s'. [%s] ERROR: truncated file?: '%s'. [%s] WARNING: Unexpected block structure in file '%s'. Possible output corruption. [%s] ERROR: fail to read the header from '%s'. main_cath:o:Usage: samtools cat [-h header.sam] [-o out.bam] [...] zRx 4  4T*  t /Users/macleand/bioruby-samtools/ext/samtools-0.1.18//usr/include/securebam_cat.c_string.h ]     - 7 w w        :! : `k n       t " 4* ? ^ a    n  -    I w   F P       7 Pu a t   '    !   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' I : ; I I : ; .: ; ' I4: ; I : ; .: ; ' .: ;' I.: ; ' I@ : ; I4: ; I , U &I : ; !$ > "I#!I/$ : ; % I: ; 8 &I' 'I(I: ; )< *!I/ +I: ;, : ; - I: ; 8 . : ; / : ;0 I: ;8 1 I: ; 8 UUN STTN V@$K$UK$Q$UQ$&^@$K$TK$N$TN$&S<mpileup __inline_strncpy_chkjprintwkputsnUkputcisspacezgroup_smplmplp_funcbam_mpileuptolowertoupper isascii8read_file_listkputs_pileup_seq__inline_memset_chk __inline_memcpy_chk__istype<read_file_listisspace__istype`$%%&%%%&r%s: %s No files read from %s RGgroup_smplbam_plcmd.cq[%s] Read group %s used in file %s but absent from the header or an alignment missing read group. -[%s] fail to load index for %d-th input. mpileup[%s] malformatted region or wrong seqname for %d-th input. [%s] %d samples in %d input files wuw##samtoolsVersion=%s 0.1.18 (r982:295)(%s) Max depth is above 1M. Potential memory hog! <%s> Set max per-file depth to %d %s %d %c %d * * *%d(%s) Fail to open file %s. Continue anyway. bam_mpileup%sAgf:r:l:M:q:Q:uaRC:BDSd:L:b:P:o:e:h:Im:F:EG:6OsUsage: samtools mpileup [options] in1.bam [in2.bam [...]] Input options: -6 assume the quality is in the Illumina-1.3+ encoding -A count anomalous read pairs -B disable BAQ computation -b FILE list of input BAM files [null] -C INT parameter for adjusting mapQ; 0 to disable [0] -d INT max per-BAM depth to avoid excessive memory usage [%d] -E extended BAQ for higher sensitivity but lower specificity -f FILE faidx indexed reference sequence file [null] -G FILE exclude read groups listed in FILE [null] -l FILE list of positions (chr pos) or regions (BED) [null] -M INT cap mapping quality at INT [%d] -r STR region in which pileup is generated [null] -R ignore RG tags -q INT skip alignments with mapQ smaller than INT [%d] -Q INT skip bases with baseQ/BAQ smaller than INT [%d] Output options: -D output per-sample DP in BCF (require -g/-u) -g generate BCF output (genotype likelihoods) -O output base positions on reads (disabled by -g/-u) -s output mapping quality (disabled by -g/-u) -S output per-sample strand bias P-value in BCF (require -g/-u) -u generate uncompress BCF output SNP/INDEL genotype likelihoods options (effective with `-g' or `-u'): -e INT Phred-scaled gap extension seq error probability [%d] -F FLOAT minimum fraction of gapped reads for candidates [%g] -h INT coefficient for homopolymer errors [%d] -I do not perform indel calling -L INT max per-sample depth for INDEL calling [%d] -m INT minimum gapped reads for indel candidates [%d] -o INT Phred-scaled gap open sequencing error probability [%d] -P STR comma separated list of platforms for indels [all] Notes: Assuming diploid individuals. zRx 4N  ,T1 4 4  /Users/macleand/bioruby-samtools/ext/samtools-0.1.18//usr/include/usr/include/securebam_plcmd.cctype.h_string.hkstring.h    & P Z d n       " P ^ q              % 1 = P c v         ) J s   V C      + D ] v        # : S l        0 I b y         - d r~ r      ," C c ~  ~       '  5  >  r y              <  @$} K$ K$ Q$ `$ $ $ $ $ $ $ $ % % P% i% n% % % % % % % % &Vread_file_listrisspace__istype%X-%g-%{-$V-$-$W-z$h-p$_-T$<-$H-($@$?$>#-#-#-#-#-#]-#-#Y-z#a-n#-b#-Y#q-M#w-A#p-5#-)#-#-#-"-"j-"u-"-"-">"="O=m"l-I"l-"V-"<y!- I-e ----5`---;-:-9-b-6---]-2-- S-R-*-Q=R-d=-S-*-Q=--S-}R-\e=%d=--V-N8-7v--m-D--o-s-r-Vv-N-8m-o-s-ie=-{---h--b-6--M-/t-* y-x--L-65---\-;-z-.43-qc-@-3,,2"O=-,1O=b-0- ,/O=---Y-t[-h^-f-\-n-i-SZ-.-&- -P= - . - - O= - - , +| O=[ k-/ - - -@ M-. 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@Bdo_swap tmp i j 49 unsigned intuint32_t7ks_ksmall_uint32_tks_ksmall_uint32_t PJVn arr kk > low t k P] pJhigh ll hh mid t t t .t Mt l%t  BHt bcf_call_del_rghashbcf_call_del_rghash4PV_hash3q  ck5>hash6 ;>kh_destroy_rg h  khint_tz kh_get_rg >Vh  key R    inc >^Kk >i >last > 1 : __ac_X31_hash_stringQ>sPJ hR>q kh_resize_rg _ Vh  _new_n_buckets >j >t > _ new_flags 2   key R val :  inc >k >i >V D tmp R  D s   __inline_memset_chkRq __destQq __valQ__lenQ! bcf_call_add_rgbcf_call_add_rgq ` <V_hashq hdtextJ MlistJ  < sJ P pJ qJ rJ tJ hash   lplqxk k%>ret&# A * d m  khint32_tp! char: B J kh_cstr_t R :  ( !n_buckets> #!size> #!n_occupied> #!upper_bound> # !flags2  #!keysc  #!valsk  # s kh_rg_t  "kh_init_rg  # kh_put_rg >h  key R ret <x >inc >k >i >site >last >ks_introsort_uint32_tks_introsort_uint32_t @Vn a  g top P stack P d _rp swap_tmp s t i j k 4TX intDbcf_call_gap_prepbcf_call_gap_preprP2VnpKn_plpp<plpppospbcapc\refpJ $rghashqq  P2 rights max_inss|X ref2uk ~ queryuk jsksleftsscore1s<score2s<max_ref2sNtKtl_runtref_typetn_alttref_sampleuhashv @p}rg~ qk>%0n_totn_alt auxPmax_rd_lensmssisn_typessts typess<P 5pc ref0k P9Ḽmax_i̭max2_i̭cnsmaxmax2rk ppbcigarseq܋xݭyݭ op߭jlc<cC inscnsuk Pinscns_aux<h`Zp {Zseq c 0maxmax_kia<hm*l/ir/apf10apf20%`pFqbegGqendGtbegGtendGscGkkGseqHcigarI%qual[bq[qq\&U%&Q&&&R &&lT' D ~!4 i.!>!h(D!4"5!!h!!i)tmpR/sc<sumq<%'psct<indelQ1indelQ2seqQindelQ&|*$+&|,, px#est_indelregdposcrefcJ lcins4ck iejemaxemax_iescoreetoupper<_c;#|tpos2qpos?c>cigar>tpos>is_left>_tpos>k@x@y@last_y@opClD#est_seqQ\bca[cl[l_run[q]qh]__inline_memcpy_chk<q __dest;q __src;q __len;ks_shuffle_uint32_tks_shuffle_uint32_t P22Vn  a G i Ub2 22j  22tmp *+! ,-__ac_prime_list} `elong unsigned intsize_t5+*,double* |?!leftq @#!rightq @#!depthA#.Dks_isort_stack_t|int32_t# o !tid#!pos#/bin#/qual#/l_qname#/flag# /n_cigar# !l_qseq#!mtid#!mpos#!isize#bam1_core_to+,short unsigned intuint16_t20__errmod_coef_t !depcorr* #!coef #errmod_t&1N__bcf_callaux_t` !capQ #!min_baseQ #!openQ #!extQ # !tandemQ #!min_support #!min_frac*#!max_bases# !indel_types#$!maxins#4!indelreg#8!inscnsk #@!bases#H!e$#P!rghashq #X,bcf_callaux_tNunsigned charkuint8_t-| 8!coreo#!l_aux# !data_len#$!m_data#(!data#0bam1_t23b#3qpos#3indel# 3level#4is_del#4is_head#4is_tail#4is_refskip#4aux#.bam_pileup1_tk float  !d #!e #!bw!#kpa_par_tj% R .@: ; ' ? 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