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42 ` SamtoolsAdapter.o/ moc_SamtoolsAdapter.o/ /0 0 0 0 644 617480 ` ELF>@@   !#%&(*,./0245689;=?ABCEFGIKLNPRTVXZ\^_`bcefhjlnprtuwyz|~UHHH}HuHUHEHHUH}umE‹E9u EI{E‹E9u EI\E‹E9u EI?E‹E9u E "E‹E9u E]UHATSHP}HudH%(HE1E w}HHHcHHHEHHHHE HUHEHDeHEйH5HHEUHuAA DHHUHEHHHEHHEHHMdH3 %(t4-HHEHHHEHHHHP[A\]ÐUHSHhH}HuHUdH%(HE1HEHHUHEHHE؅t&HEHPHEHHHtHEHHHEE؅trHEHUH։EHE@E ЉEHEHH8HHUHЄtDHMHEHHEHEHHE؃EHEHu.+HHEHHHEHHHHEHMdH3 %(tHh[]ÐUHSHXH}HuHUdH%(HE1HEHE̋MHEHEE;E EȍHEHHEHUHEHHHHENjEXHEH9tDEPHEHHEHUHEHHHHEHEHH8HHUHЄuQ]NjUHEHHEHUHEЉHEHHEHHHHEHMdH3 %(tHX[]ÐUHSHXH}HudH%(HE1HEHHUHEHHE؅t&HEHPHEHHHtHEHHHEE؅_HMHEHHHE@HEHHE@= sizeof(QArrayData)/usr/include/x86_64-linux-gnu/qt5/QtCore/qbytearray.huint(i) < uint(size())i >= 0/usr/include/x86_64-linux-gnu/qt5/QtCore/qstring.h&other != thisInvalid cigar operation %1, cannot convert to samtoolsSamtools: missing colon in auxiliary dataSamtools: parse warning: integer %1 is out of range.Samtools: length of the hex string not even.Samtools: invalid hex character.Samtools: too few values in aux type B.Samtools: unrecognized array type.Samtools: unrecognized type.Internal SamtoolsAdapter seq check failed: expected length %1, got %2Internal SamtoolsAdapter seq check failed: expected %1, got %2 at pos %3Internal SamtoolsAdapter qual check failed: expected length %1, got %2Internal SamtoolsAdapter qual check failed: quality out of bounds: data_len is %1, but last qual offset is %2Internal SamtoolsAdapter qual check failed: expected %1, got %2 at pos %3!*=/usr/include/x86_64-linux-gnu/qt5/QtCore/qvector.hasize >= 0 && asize <= aallocx->ref.isSharable() || options.testFlag(QArrayData::Unsharable)!x->ref.isStatic()int(d->alloc) == aallocisDetached()x == dd->data()uint(d->size) <= d->allocd != Data::unsharableEmpty()aalloc ? d != Data::sharedNull() : d == Data::sharedNull()d->alloc >= uint(aalloc)d->size == asizeAlgorithmsConsoleCore ServicesInput/OutputPerformanceScriptsTasksUser InterfaceUser 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( ( 6 D S x ^ @`t.symtab.strtab.shstrtab.rela.text.data.bss.rodata.rela.debug_info.debug_abbrev.rela.debug_aranges.rela.debug_line.debug_str.comment.note.GNU-stack.rela.eh_frame @@(&(,(1(>9_9@0J] 0X@0 q l@( }0 L0 5P P @@xX `bam_import.o/ 0 0 0 644 42736 ` ELF>@@UH}umE‹E9u EI{E‹E9u EI\E‹E9u EI?E‹E9u E "E‹E9u E]UH}}Ct }ct}Au1}St}su}It }it}fu]UHH}HEE}t1HEE+EHEЉEHEHEu֋E]UHH H} HEHEHUHP@HHEHHEUHHH}H}tHEHHHEHUHHH}HE@tHEPHE@ 9| HEPHE@ 9|^HE@HEHHEH@@HHHEP HE@ =? HE@HE@ u#HEH0HE@HHUJHHUHH0H}uHUHMDEH}t HE}t HEHHUHHEPHE@ 9|HE@t HEPHE@ 9|jHE@QHE@HEHHEH@@HHHEP HE@ =? HE@HE@ }~?HE@E"HEHEHH;EEHE@ ;E}uTHE@E:HHEHEHHHH% EHE@ ;Ev}ufHE@ELHHEHEHHHH% tHEHEHH< uEHE@ ;E EHEHPHEHHH)HE@U)‰ЃHH9HEHHE@M)HHHPHEHPHEH@HPHEHPHEHPHEH@HH HEHPHEHPHEH@HH HEHPHEHPHEH@HH HEHPHEHPHEH@HH HEHPHEHPHEH@HH HEHPHEH@HPHEHPHEHPHEH@HHHHEHPHE@U)‰HHUH HURHcH4HUHJHUHHHHHEHHE@M)HHHEHEPHEPHE@ ;EH}tHEHEHHHEЉHEH@Hu&HEH@HHEHPHEHPHEHHHEHUHH H}uHUHMHMHUuHEAHUH(]UHHH}H}t=%ld, x=%ld,y=%ld SNSQLN*[sam_read1] missing header? Abort! 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z    ] F6 B EN +Z f r J~ { &   ]    K b E Q ] Hi  0 ) T  ` r N }     s( 4 @ IL X gd Sp | n     K   # / /< 0O >[ g 0s   l 5   # F  s  SK r~ B  Cb; }At  | l  N 0~ ` L  3 3 01  S  d z     '  ( l  t  P # V    l C R W   <U+ : I{ # #    J Z Sj z | <  =  ( S#p)P [ f )    & @b`'##.symtab.strtab.shstrtab.rela.text.data.bss.rela.rodata.rela.debug_info.debug_abbrev.rela.debug_aranges.debug_ranges.rela.debug_line.debug_str.comment.note.GNU-stack.rela.eh_frame @c*@Z &*,*6*1@hC.>@lO}?VbA0]@0 qBC@ 0rK0lR5RR @ȁSX  Ybam_pileup.o/ 0 0 0 644 29464 ` ELF>m@@UHH H}HuHEH@0HEHE@(EHE@$;E~WHE@$EmE EE EE EE EE EEEHcHEHHHEHE@$HcHEHH0HEHHHEHUH HHJHHHJHHHJHHHJ HH HJ(HH(HR0HP0HEUP(HEHUHP0HEUHHHEHEUHH H}EHHEH@UHcHHHH@0HHEH@UHcHHHHEHE@;EHEH@HHEHUHHH}HEPHEHE@uX,HEHPHE@HHEHHE@HHHHUHHH}HuHEPHEHEH@PHEPHE@9uRHE@t HE@HEPHE@HHHEH@HHHHEHPHEHpHE@HHUJHHHHEHUHHpH}uHUHEHHEHEHEHEHP0HE@ HHEEHEnEHE@fuUHEt HEtHEHEHEPHEPHE@EHEPHEPHE@EHHHEHЋEȋEHHHEHЋẼ}td}t^}tX}tR}uHEPEHEP}t}uHEPEHEPEHE@;E^HE@;EH ZH5H=HEUHEHHHEHЋEHE@‹E)Љ‹E9uHEHE@9|H `H5H=HEHHHHEHЋEԃ}t}t}t}t }HEHHHEHЋtBHEHHHEHЋt!HEHHHEHЋuHEPEHEPHEPEHEPHEPHE,HEHHHEHЋtBHEHHHEHЋt!HEHHHEHЋuHEPEHEPHEPEHEPHEEyEHHHEHЋEԋEHHHEHЋEЃ}tO}tI}tC}t=}t7}t}uHEPEHEPEHE@;EsHEUHEHE@9|H pH5H=HEHHHEHЋEHEHHHEHЋEHEPPHE@HEP HE@ HEуP ʈPHEPEЃ;ESHEPHE@97HEHHHHEHЋEHEHHHHEHЋE}uE؉HEP }uHEUP }HEPHE@9EHEEhEHHHEHЋEEHHHEHЋE}uEE}t,}t&}t }t}tEHE@;E}~ HEUP }t }t}u$HE@HE@E)ЉHEPI}t}u=HEPPHEPHEP}HE P ʈPHE@;EHE P ʈPHE@ ;EHE P ʈPUHH H}HuhHEHHEHHEHHfHHEHPHEHPHEHPHEHHHEHEHEH@PHuHEHPHEHPUHH}u}x EHEP4]UHH}uHEUP@]UHH@H}؉uHUHM8HEHUHEHHHEUHEHHUHEHHHUHEHHE}yHEHƿHEHH}tHEH@0HHEHUHHH}uHEHUHUHHH}HEHHUHH H}HuHEHHEHHEHUHPHEHUHPHEUHHH}HEHHHEHUHH0H}HudH%(HE1HEHHUHHE}y/EUHEH@HUHrUMAɋMHMIDHEHHMHUHuHHEH}uH}dH3<%(tUHSH8}HuHUȾ0HEEHHHHEHPEHHHHEHP EHHHHEHP(EHHHHEHPHEU܉HEH@EcHEH@UHcHHEHHHEHHHEHHHHEH@UHcHHHEH@HEE;E|HEH8[]UHH}uE"HEH@UHcHHHUP@EHE;EӐ]UHH H}E$HEH@UHcHHHHEHE;EHEH@HHEH@HHEH@ HHEH@(HHEHUHSHXH}HuHUHMLEdH%(HE1EHEE HEH@UHcHHHHEH@H9HEH@(UHcHHHEH@ UHcHH HEH@UHcHHHHUHuHHHEH@UHcHHЋUHcHH UHcH HHEH@(UHcHHHHt:HEH@UHcHHHH;EsHEH@UHcHHHHEEHEȋ;EHEHUHPH}u HEH HEHEHEEHEH@UHcHHHHEH@H9ubEHHHEHHEH@ MHcHHȋEHHHEHHEH@(MHcHHHHE5EHHHEHEHHHEHHEHEȋ;E1EH}dH3<%(tHX[]src/samtools/bam_pileup.ck < c->n_cigars->k < c->n_cigar[bam_plp_destroy] memory leak: %d. Continue anyway. [%s] unsorted input. Pileup aborts. [bam_pileup_core] the input is not sorted (chromosomes out of order) [bam_pileup_core] the input is not sorted (reads out of order) bam_plp_nextresolve_cigar2 8intii0$b (08@ H P X \` bh bp  bt px F T h x !{ ) * + , .- /b 1~ \\bb+ x $   b[bi0?3M78  bfd b    b  $ b4 b8 b< b@ H P X ` !h $p $x b  % ) fpr * fpw +X $ %b & ' 'x , 0b 1b 2  3( 40 5b8 6b< 7b@ 8H 9P :6 tidposbin  8Òb b$b(0Ɲb  b bauxbhmpu d d d tid pos$(,b0b4b8b<b@plp{ HbPX`0v nwbminxposx  y  z plp{ (!b@b@F #| $ %  &'K kbxbybendb  X  bbeg8end<s@ P^ cntbnbmaxbbuf^ d  ' j @ XPhbdu !! mpu h!!X "mp!u X k#bl#+d e "mp+u h!1 "mp1u h"p1d `#Cb36 "pC{ "posC"sC6  bHX cI< `$Jh kKb$Kb%R & opTb lUb& op^bD l^b@' optbH ltbL'7 op2xbP l2ybT' l3}b R  B ( )X)P$h* )h(@j )H)@))%z +$b\ pd ` qd h z j (bw )X"bP, @L) X P H @-plp @h.!q!X-p#d `-q#d h//*/h/bd/44h4bd,=bv0fp=H=bD= =-buf?vh-ret@b\-bA`|.M&0bufMvhMbd.R0bufRvh,WvZ7W XWP-bufYvh.a*e0bufavh,gb0bgH0bufgv@-retib\ibP-tidibT-posibX-plpj@`,~/Z0n~bL~@~Z-ibTX/DXbT-ibl.X-ibl,b0plp -ibH-retbLP'-tidb@-posbD$  1b% : ; I$ > $ >   I : ;  : ; I8 : ;I8 : ; I !I/ &I : ; I8  : ;  : ; I : ;  : ; I 8  : ; I 8  : ; : ;I8  : ;I 8  : ;I 8 : ;I'II : ;.: ;'I@B: ;I4: ;I.: ; I@B 4: ; I!.: ; '@B": ; I#.: ; 'I@B$4: ; I%4I4& ' (.?: ; 'I@B): ; I*.?: ; '@B+ U,.?: ;'I@B-4: ;I..?: ;'@B/.?: ;'@B0: ;I14: ; I?<,9 A src/samtools/usr/lib/gcc/x86_64-linux-gnu/5/include/usr/include/x86_64-linux-gnu/bits/usr/include/usr/include/x86_64-linux-gnu/sysbam.hbam_pileup.cstddef.htypes.hstdio.hlibio.htypes.hstdint.hknetfile.hbgzf.h 󻟻>>Kz./K0$J>,0!Xu/* <2wu (%fffgfKff)JCJ#ffff//>//8ffffgff+JAJ>Gt##f/fu8fffffcJfffg$fgJY./=*uK1'$?u=Jw=!3JYXu8&@wJ< =#K%K'uYf]X #t"Y1t <B7#Y#XKZYwv=##a$#gZ1׻Y?fXu?Cj/g/-tY1=??/K1?fZ*&Yt?/?JKwJ?$@?u)W.zJt%\g5J=__off_tshort int_IO_read_ptrmp_freeblock_addresssize_t_shortbufisize_tidmpostypebam_plp_auto_fpathmax_plpbsrcbam_mplp_set_maxcntctrl_fdnextbam_mplp_destroyresolve_cigar2responseint16_tbam_mplp_tsigned char__PRETTY_FUNCTION__quallong long unsigned intqposflag_mask_fileno_IO_read_endbam_plp_destroyblock_offsetlong intnew_minuncompressed_block_flags_IO_buf_end_cur_columnmaxcntlong long intn_cigar_lockis_eof_old_offsetbam1_tknetFile_sbam_plp_set_maxcntcache_sizemp_allocbam_plbuf_tmaskis_ready__pad3dummyGNU C11 5.4.0 20160609 -m64 -mtune=generic -march=x86-64 -g -fPIC -fstack-protector-strongportbam1_core_tn_plp_IO_markerhostpasv_port__bam_plp_tunsigned intmax_responsebam_plbuf_set_maskBGZFlong unsigned int_IO_write_ptr_sbufleveldatashort unsigned intsize_cmdfile_descriptorbam_plp_init_IO_save_baseseek_offsetsrc/samtools/bam_pileup.cno_reconnectbam_plbuf_init_moderetrbam_plp_nextbam_plp_autohttp_hostcigarblock_lengthis_dell_qnamebamFilebam_copy1tailsizetypelbnode_tmp_destroymtidbam_pileup1_tl_qseq__linkbuf_t_IO_write_enduint64_t/home/birch/BIRCH/local/pkg/ugene-1.29.0/src/libs_3rdparty/samtoolscompressed_block_sizebam_plbuf_reset_IO_lock_titer_IO_FILEmp_initbam_plp_reset_poserroropen_mode_markerspasv_ipbam_plp_set_maskint32_tunsigned charg_cstate_nullbam_plp_pushbam_plp_t_chain_flags2knetFileflagcompressed_block__func__data_lenFILEbam_plbuf_pushcorebdstbam_plbuf_destroyheaduint32_tbam_mplp_initcstate_tmempool_tfunc_dataindelcharfunc_offsetbam_mplp_automax_pos_next__off64_toffset_IO_read_basebam_pileup_f_IO_save_endbam_pileup_fileis_head__pad1__pad2is_refskip__pad4__pad5m_data_unused2stderruncompressed_block_sizeowned_file__bam_mplp_tuint8_t_IO_backup_base_vtable_offsetmax_tidint64_tcompress_levell_aux_IO_write_baseis_tailcache_IO_buf_base_n_plpfile_sizeGCC: (Ubuntu 5.4.0-6ubuntu1~16.04.5) 5.4.0 20160609zRx AC  <!AC \ \AC  |eAC ` AC  3AC . 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[%s] malformatted region or wrong seqname for %d-th input. [%s] %d samples in %d input files wuw0.1.18 (r982:295)##samtoolsVersion=%s (%s) Max depth is above 1M. 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RG[bam_merge_core] '%s' is truncated. Continue anyway. Usage: 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. @HD SO:@HD VN:1.3 SO:%s SO:%s%s.%.4d.bam%s.bam[sort_blocks] fail to create file %s. [bam_sort_core] fail to open file %s querynamecoordinate[bam_sort_core] truncated file. Continue anyway. [bam_sort_core] merging from %d files... Usage: samtools sort [-on] [-m ] bam_merge_corebam_merge]_L?C G8intii?b?iF /. @    4 0D  ?     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S@' E U 1d o N9@`Jql]?o0X@0 qoo l@  }0|! 0%5Z`@8H  Hbam_stat.o/ 0 0 0 644 14952 ` ELF>(5@@UHH0H}ؾHE8HEHEHEHE@ %EHEUHcHHHHEUHcH HE@ HEUHcHHHHHEUHcHH HE@ t(HEUHcHHHHHEUHcHH HE@ @t(HEUHcH HHHHEUHcH H HE@ %t(HEUHcHHHHHEUHcHH HE@ t:HE@ u(HEUHcH HHHHEUHcH H HE@ HE@ HEUHcHHHHHEUHcHH HEPHE9t\HEUHcHHHHHEUHcHH HE@ <v(HEUHcHHHHHEUHcHH HE@ u(HEUHcHHHHHEUHcHH HE@ %t(HEUHcHHHHHEUHcHH HUHEHHE}4H}tHEH@0HHEH}t#HHH5H=HEUHH0}HuH9Eu-HHH"H=HHHHEHHH5Ht.HHHHEHHH5H HHHH5HEH}uH ;H5H=HEHHEHEHHEHEHPHEHHH=HEHHEHHH=HEH@fH*HEH@fH*^Z f(YHEH@fH*HEHfH*^Z YHEHPHEH@f(HH=HEHP(HEH@ HH=HEHPhHEH@`HH=HEHPxHEH@pHH=HEH@HfH*HEH@(fH*^Z f(YHEH@@fH*HEH@ fH*^Z YHEHPHHEH@@f(HH=HEHP8HEH@0HH=HEH@XfH*HEH@(fH*^Z f(YHEH@PfH*HEH@ fH*^Z YHEHPXHEH@Pf(HH=HEHHEHHH=HEHHEHHH=HEHHEHHEH[bam_flagstat_core] Truncated file? Continue anyway. Usage: samtools flagstat -rsrc/samtools/bam_stat.cfp%lld + %lld in total (QC-passed reads + QC-failed reads) %lld + %lld duplicates %lld + %lld mapped (%.2f%%:%.2f%%) %lld + %lld paired in sequencing %lld + %lld read1 %lld + %lld read2 %lld + %lld properly paired (%.2f%%:%.2f%%) %lld + %lld with itself and mate mapped %lld + %lld singletons (%.2f%%:%.2f%%) %lld + %lld with mate mapped to a different chr %lld + %lld with mate mapped to a different chr (mapQ>=5) bam_flagstatY@R int^^B%P&W(^0-3;0t W     ( 0 8 @ H P X ` h Wp  Wt ex 4 I   !p ) * + , . /W 1    W{  {t  { WfdW    W $ W4 W8 W< W@ H P X  ` !h $p $x W {%)fpr*fpw+X$ %W & ' 'x, 0W 1W 2 3( 40 5W8 6W< 7W@ 8H 9P: 6H WT X YT ZZ [ [ [( \0 \8 ]@ ^ tid pos bin           k8 W  W W$ W( W0 ]    0 @ P ` p       { n!]fp!Hs#Xb$h`c%hret&WPw+WT 1W51WL1T@fp3X4`s5h/ ` / {  GW% $ > $ > : ; I  I&I : ;  : ; I8 : ;I8 : ; I !I/  : ; I8  : ;  : ; I : ;  : ; I 8  : ; I 8 .?: ; 'I@B: ; I4: ; I : ; I4: ; I4I44: ; I?<, src/samtools/usr/include/x86_64-linux-gnu/bits/usr/lib/gcc/x86_64-linux-gnu/5/include/usr/includebam_stat.ctypes.hstddef.hstdint.hstdio.hlibio.hknetfile.hbgzf.hbam.hgetopt.h !//YQ:( ( < (   (XX94( (<(tg#K0#0.Kt#*$$$$**Y__off_tbam_flagstat_core_IO_read_ptrn_pair_allsize_t_shortbufisizempostypepath_IO_buf_baselong long unsigned intn_sgltndatactrl_fdbam_header_tresponseint16_tlong long intsigned charn_diffhigh__PRETTY_FUNCTION__n_diffchrqual_fileno_IO_read_endint64_tlong int_flags_IO_buf_end_cur_columnshort intn_cigarl_text_lock_old_offsetbam1_tknetFile_scache_sizesrc/samtools/bam_stat.cm_datais_readyGNU C11 5.4.0 20160609 -m64 -mtune=generic -march=x86-64 -g -fPIC -fstack-protector-strongtarget_nameportbam1_core_t_IO_markerstdinpasv_portuncompressed_blockunsigned intmax_responseBGZFlong unsigned int_IO_write_ptr_sbuftarget_lenshort unsigned intsize_cmdfile_descriptorn_pair_map_IO_save_baseseek_offsetno_reconnect_flags2_moden_read1n_read2retrhttp_hostn_textblock_lengthl_qnamebamFilesizetype_offsetmtidoptindl_qseqn_pair_good_IO_write_end/home/birch/BIRCH/local/pkg/ugene-1.29.0/src/libs_3rdparty/samtoolscompressed_block_size_IO_lock_t_IO_FILEbam_flagstatrg2lib_poserroropen_mode_markerspasv_ipint32_tunsigned charn_dup_chainknetFileflagcompressed_block_vtable_offsetdata_lenFILEcoreuint32_tdictn_readsblock_offsetcharblock_addresstextn_targetshost_next__off64_toffset_IO_read_base_IO_save_endhash__pad1__pad2__pad3__pad4__pad5_unused2stderruncompressed_block_sizen_mappedowned_fileuint8_t_IO_backup_baseargccachecompress_levell_auxargv_IO_write_basebam_flagstat_theaderfile_sizeGCC: (Ubuntu 5.4.0-6ubuntu1~16.04.5) 5.4.0 20160609zRx ]AC X <5AC 0  H    %]7MT^cjq]5~bam_stat.c__PRETTY_FUNCTION__.4459bam_flagstat_core_GLOBAL_OFFSET_TABLE_callocbam_read1freestderrfwritebam_flagstatoptindstrcmpbgzf_openstdinfilenobgzf_fdopen__assert_failbam_header_readprintfbam_header_destroybgzf_close**7*NSo*}*4*W*Y*Y!3D?[FsKWg|T#TEOis1T'TIDSmtwTT/9Yco{ !    ) 0 ?7 > RE qL S <a f q ~ Q  2 7  {  e     ( 4 @ L X Xd $p }   & S   [ 0 y 9 U  Z & #3 *@ 1M 8Z g ?u | $    n N   & 2 /> 5J _V b n z     S # Z  ) p5 K OW c ?o h{  4  y   l I      $ 0 N< -H a   A c F n b I C  ' 3 ? K ^ gw  g '  u |   M    !w? ]    H5 g@ /K H  @].symtab.strtab.shstrtab.rela.text.data.bss.rodata.rela.debug_info.debug_abbrev.rela.debug_aranges.rela.debug_line.debug_str.comment.note.GNU-stack.rela.eh_frame @@ &,1`>8 V9@P& Jw]0X@40 q5l@04 }0%0 5AHX@H40x40 bam_tview.o/ 0 0 0 644 5792 ` ELF>`@@UHH}HuHHHLH=[bam_tview_main] The ncurses library is unavailable; tview is not compiled.  98intiib (08@ H P X Q` Wh bp  bt px F T ] m !{ ) * + , .- /b 1s QQWb  m    b9bl`W% : ; I$ > $ >   I : ;  : ; I8 : ;I8 : ; I !I/ .?: ;'I@B: ;I4: ; I?<,9 src/samtools/usr/lib/gcc/x86_64-linux-gnu/5/include/usr/include/x86_64-linux-gnu/bits/usr/includebam_tview.cstddef.htypes.hlibio.hstdio.h #Y_IO_buf_end_old_offset_IO_save_endshort intsize_tsizetype_offset_IO_write_ptr_flags_IO_buf_base_markers_IO_read_end/home/birch/BIRCH/local/pkg/ugene-1.29.0/src/libs_3rdparty/samtoolsstderrsrc/samtools/bam_tview.c_locklong int_cur_column_posargv_sbuf_IO_FILEunsigned charargcsigned charunsigned int_IO_marker_shortbuf_IO_write_base_unused2_IO_read_ptrshort unsigned intGNU C11 5.4.0 20160609 -m64 -mtune=generic -march=x86-64 -g -fPIC -fstack-protector-strongchar_next__pad1__pad2__pad3__pad4__pad5long unsigned int_IO_write_end__off64_t__off_t_chain_IO_backup_base_flags2_mode_IO_read_base_vtable_offset_IO_save_base_filenobam_tview_main_IO_lock_tGCC: (Ubuntu 5.4.0-6ubuntu1~16.04.5) 5.4.0 20160609zRx 9AC t     929bam_tview.cbam_tview_main_GLOBAL_OFFSET_TABLE_stderrfwrite*).    ) . /; B I }P 6W *^ %l q C| 9 6   U p r p X G + \   " R/ < iI KV c bp }  ~ N  ?      j  g ! 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K XW c o {  4   e 3 >   G$ T ` !l   x   *     O #) 5 A M RY e x   s *  B& rB Q ` *} 7 B G w 1 =  1+ < =Y Gd [o Hz  * / @s`.symtab.strtab.shstrtab.rela.text.data.bss.rela.rodata.rela.debug_info.debug_abbrev.rela.debug_aranges.rela.debug_line.debug_str.comment.note.GNU-stack.rela.eh_frame @ @& &` ,` 6` 1@1Cl >@x3Ob0]@8C0 vOq@hC 0-00 5e h @CHC  %4sam.o/ 0 0 0 644 21384 ` ELF>N@@UHSH(H}ظHEHEHUH HHJHHHJHHHJHHHJ HH HJ(HH(HJ0HH0HJ8HH8HR@HP@HEH@(HEHP(HEHPHEHPHEHP HEH@0HHHHEHP@HEHP0HEHH@HEH@@HHHEHHHHEHPHEHHHHEHPEkHEH@UHcHHHEH@MHcHHȋHEH@UHcHHHEH@UHcHHHHHEHE;EHEH([]UHH0H}HuUHEH@0EHEH@0‹EЃEH}mE EE EE EE EE EEmE EE EE EE EE EEE;E}$EHcHEH@@HHHHEHP@EHcHEHH@HEH@0HHEHHHEHP0EHHHEHP0HEHP@HEH@0HUHH`H}HuHUdH%(HE1HEHHHErHH5HE؋HE؉HEbHHHE؋HE؉HEH5HtHEH5HH#HHHH5HHEHPHEH@HYHEH@HHHEHP3HEHHHEHPHEH@HHEH@HHHEHPHEH@HuHEHHEH@H}teHEH@HEHEHHHEHPHEH@HHEH@0HEHH@HEH@HHHEHHEH@=H,HHH&H=HHEH@HHH5HǸHEwHHHEHHHEHPHEbHHYEE,EHcHEH $ >  I&I &  : ;  : ; I8 : ;I8 : ; I!I/  : ; I8  : ;  : ; I : ;  : ; I 8  : ; I 8 : ;I< : ; : ;I8  : ;I 8  : ;I 8 'II : ; I.?: ; 'I@B: ; I 4: ; I!.: ; '@B": ; I# : ; $ U%4: ; I& '.?: ; '@B(4: ; I?<)4: ;I?<,x z: = = @ % src/samtools/usr/lib/gcc/x86_64-linux-gnu/5/include/usr/include/x86_64-linux-gnu/bits/usr/includesam.cstddef.htypes.hstdint.hstdio.hlibio.hknetfile.hbgzf.hbam.hsam.h  N,$#.9JKv/K44$(uzt'1</ft#gɻ!ug% ( -gu<<JX!<XuXuft%fJX/X/(v-t%SJ@f@ < ? 3 ? @ # #$ *H 9Y p B C C *'  ) *& *'! & (2 D> *'U Z (f #    ) . #; tB VI ] i Qp Ow ~ r  ) I    s    3 # / :; BG S _ [k ?w   U -     K  / f _  o- v: G T a n |   #   h Q  3 ! - 9 6E 9Q b] i u      V (  $ #0 < &R ^ j v   9  }  Y o N     b+ 7 _C 2O h   F  W z g D > " . : F R e lp I      g Q } l% |7 C< H # :   * 9 Q  ~ s* 4| _ ~   6 5< A E N >] 0f \ &  h _  9 C w s   C  : ' 1  H V +e 3p {   g  Ddh  w C  .symtab.strtab.shstrtab.rela.text.data.bss.rodata.rela.debug_info.debug_abbrev.rela.debug_aranges.debug_ranges.rela.debug_line.debug_str.comment.note.GNU-stack.rela.eh_frame @x @X1 & , 1 A> 9@H;JC]0X@@L0 l `i)z@pL 0 0!'5V'X' @LHMx(x .csam_header.o/ 0 0 0 644 38280 ` ELF>@@UHH}HEE}t1HEE+EHEЉEHEHEu֋E]UH(]UHHH}H}tHEH@HUHHjHHEHPHEHH=HEHEHEHEt HE< tHEtCHUHEH)HHt/HUHEH)HЉHEHH=HEHEHECHEUHH0H}HEHHHkE}u2HE@HEH=EHUHcHЋUHcHHHHEHHHHE@HEHUHcHЋUHcHHHHHuHcHuHcHHHAH=S EHUHcHHt*HUHcHЋUHcHHHHHEH@HEHEH@HEHUHcHHEHHukHUHcHHEHHuGHE@HEHE@HEAH=`HEH@HEH}NUHH H}HuHEH@HEHE@HEHEH5HǸHEH@HEHEHƿ HE< u HE@< t-HE@HEHEH5HǸHEH@HUHHHEH@HEH}qHEHƿ UHH H}HEH@HE4HEH@HEHEH@HHEHHEH@HEH}uHEH@HHEHUHH H}HEHEHEHEHEH@H^HEH@HEH}uHEHdUHH H}HE:HEH@HEHEHHHEHHHEHEH@HEH}uHEUHH`H}HEHEHEEEHEHEHEH@HEHEH@HEEiHEH@HEHEH@H‹EЃEHE< u HE@< tHEH@H‹EЃEHEH@HEH}uHEH@HEH}[EEHHHEHEHE<HEH@HEHEH@HEHE@HEMHcHMH<щH5EHEH@HEEHcHEHf EHE< u HE@< t;HE@HEMHcHMH<щH5EHEH@UHcHUHHH5HϸEHEH@HEH}BHEH@HEEHcHEHf EH}EHcHEHHEUHHPH}dH%(HE1HEHEHEEH}u HEHEHEHHEH}t/}tHEHtHUHEHHHE;H}t HEHHEHHEHt HEH?HUHMHEHHHEH}YHEHt HEHHEHMdH3 %(tUHH`H}HuHUHMdH%(HE1HEHEHEHEȸHEH}$HE*HEH@HEHEHE8uHEPHEH8tHEH@HEHUHEHHHEHUHEHHHEH}tH}uHEH@HEHEHPHEHH8EHE؋;EtHEH@HH=mHEHHHUHEHHEHEH@ UHHHEH@HHEH@HEH}HEHMdH3 %(tUHHPH}HuHUHMHEHEHEHEHEEEԉEHEUЉHEH@HEHEHE8uHEPHEH8tHEH@HEHUHEHHBHEH}uHEH@HEnE;Eu5}tEEЋEHHHEHHHEEԍPUHHHEHHEH@HHEH@HEH}HEUԉHEUHH H}HuHEHEHUHEHH2EHE;EtHEH@ UHHHUHH}HEHEH}t HE@]UHH H}HEHEHEHmUHH@}HuHEHE} oHEHHHEE@EHHHEHHHEHEHEEHEHPHEH@HHE܃}uHEH@HE}uUHEHPHHHHHEHPHHHHH=}uHEHPHEH@HHNE H};}u&HEH@HDHHEHHHEHEH@HEH}EE;EHE 5a 0`   0 ` Y0`p= ף?SOGOVNASM5URSPSNLNCNDSDTFOKSLBPGPIPLPUSMIDCLHDSQRGCO[nextline] Insufficient memory! 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V $Ur $J  $_ k $ $ $O $ $-+ $; $uF ] $Ul $J  $ u $ $} $L & $f5 $D g $Br u $ $U $ $O $  $U $J3 $OB $R $Y ~ $U $J $  $U $J  $ A. $= $L $Cb $m  $  $U $  $ $/ $? $CO%d $Us $JC $U $JJ $O % $5 $CD $US $^q $ $ $}! $ $o $p $z $=!N $Ul $K} $d# $ $o $p $%a#6 $UE#h $s[$ $x$ $3 $= $H$m $,} $ $ $t $%B% $b% $ $, $[8F $R] $ g $5 $C/ $0 $%1 $N2 $)3 $'40 $<5E $Q6Z $f7o ${8 $=9 $: $X; $#<  @Q`f+L  Z @ `2  Vk u@u`A O @}!`#[$$$$.symtab.strtab.shstrtab.rela.text.data.bss.rodata.rela.data.rel.local.rela.data.rel.rela.debug_info.debug_abbrev.rela.debug_aranges.debug_ranges.rela.debug_line.debug_str.comment.note.GNU-stack.rela.eh_frame @&@b &&,&1&h >`* 9@lS, N@xob,]@hp nA(D0|@0 XD0D@ 0K0S5ESHS@8 @W( ^4sam_view.o/ 0 0 0 644 45200 ` ELF>Ъ@@UHH H}uHUHEHEHHHPHEH@H9HEHEHHHPHEHPHEH@HPHEHPHEHPHEH@HH HEHPHEHPHEH@HH HEHPHEHPHEH@HH HEHPHEHPHEH@HH HEHPHEHPHEH@HH HEHPHEH@HPHEHPHEHPHEH@HHHHEHPEHcHEHHHEHHHEHHHEHEHHHEHHEHPHEHHEUHH}HuHEHHPHEH@H9HEHHPHEHPHEH@HPHEHPHEHPHEH@HH HEHPHEHPHEH@HH HEHPHEHPHEH@HH HEHPHEHPHEH@HH HEHPHEHPHEH@HH HEHPHEH@HPHEHPHEHPHEH@HHHHEHPHEHpHEHHHHUH HUHEHPHEHHEUHH}HEE}t1HEE+EHEЉEHEHEu֋E]UH(]UHHH}H}tH=HHH;H=HHHJH=HHHHH=HHH<H=HHH,H=HHH=H=HHH1H=HHH2H=HHH.H=HHH:H=HHH=H=HHHPH=HHHH=HHHƿ }t#HHHAH=UHH }Hu}t-HHH5H=EHEHEHHHEHPHHHEHPHEH@HHEHPHHHEHP HEH@HHEHP(HEH@HHUEH։EHEHEUHHP}Hu}u-HHH H=HEHHH5HtHEHHH5H HHHH5HEH}u yHEHHE8HEHEEHE@EԿ@HHHEH@0HHHE@ @t"HE@ %uH=>HE@ %t HE@ @uH= Eԃ;E~VEԃẼmE E̋E E̋E E̋E E̋E ẼEEHcHEHHHE؋EHcHEHHEHP0HE@HcHE@ HHHEESEHcHEH4EЉHcHEHEЙЃ)к)‰EE;E|HE@ EvEԃ+EHcHEHHHEʋEԃ+EHcHEH EHcHEHHHEHcHEHEʈEE;EEԃt0EHcHEH EHcHEHHHE7EHcHEHHHEHcHEHHHEE;E|HEHH=HEHP0HE@HcHE@ HHE@HHHHEE&EHcHEHЋUHcHUH!EE;E|HE@ thEUEԃ+EHcHEHEˋEԃ+EHcHEH‹EHcHEHEHcHEHEˈEE;EHEHHUHEHH HEHH}tHEH@0HHEHHEHHEH     5a 0`   0 ` Y0`p= ף?RG@RG ID:Sbct:h1Ho:q:f:F:ul:r:xX?T:R:L:s:r%s[main_samview] fail to open "%s" for reading. [main_samview] fail to read the header from "%s". -standard output[main_samview] fail to open "%s" for writing. [main_samview] truncated file. [main_samview] random alignment retrieval only works for indexed BAM files. [main_samview] region "%s" specifies an unknown reference name. Continue anyway. [main_samview] retrieval of region "%s" failed due to truncated file or corrupt BAM index file %d Usage: samtools view [options] | [region1 [...]] Options: -b output BAM -h print header for the SAM output -H print header only (no alignments) -S input is SAM -u uncompressed BAM output (force -b) -1 fast compression (force -b) -x output FLAG in HEX (samtools-C specific) -X output FLAG in string (samtools-C specific) -c print only the count of matching records -L FILE output alignments overlapping the input BED FILE [null] -t FILE list of reference names and lengths (force -S) [null] -T FILE reference sequence file (force -S) [null] -o FILE output file name [stdout] -R FILE list of read groups to be outputted [null] -f INT required flag, 0 for unset [0] -F INT filtering flag, 0 for unset [0] -q INT minimum mapping quality [0] -l STR only output reads in library STR [null] -r STR only output reads in read group STR [null] -s FLOAT fraction of templates to subsample; integer part as seed [-1] -? longer help Notes: 1. By default, this command assumes the file on the command line is in the BAM format and it prints the alignments in SAM. If `-t' is applied, the input file is assumed to be in the SAM format. The file supplied with `-t' is SPACE/TAB delimited with the first two fields of each line consisting of the reference name and the corresponding sequence length. The `.fai' file generated by `faidx' can be used here. This file may be empty if reads are unaligned. 2. SAM->BAM conversion: `samtools view -bT ref.fa in.sam.gz'. 3. BAM->SAM conversion: `samtools view in.bam'. 4. A region should be presented in one of the following formats: `chr1', `chr2:1,000' and `chr3:1000-2,000'. When a region is specified, the input alignment file must be an indexed BAM file. 5. Option `-u' is preferred over `-b' when the output is piped to another samtools command. 6. In a string FLAG, each character represents one bit with p=0x1 (paired), P=0x2 (properly paired), u=0x4 (unmapped), U=0x8 (mate unmapped), r=0x10 (reverse), R=0x20 (mate reverse) 1=0x40 (first), 2=0x80 (second), s=0x100 (not primary), f=0x200 (failure) and d=0x400 (duplicate). Note that `-x' and `-X' are samtools-C specific. Picard and older samtools do not support HEX or string flags. Usage: bamtk import import-o-btUsage: samtools bam2fq /1/2+p= ף??V-?@ (8intii?[b?i0o ?     ( 0 8 @ H P X ` h ?p  ?t px T [   !{ ) * + , .- /? 1    ?v  o   0M 3F  ?fd ?    ? $ ?4 ?8 ?< ?@ H P X ` !h $p $x ?  % )fpr *fpw +!X $ %? & ' 'x , 0? 1? 2 3( 40 5?8 6?< 7?@ 8H 9P :' 6H Ws X Ys Zy [ [ [( \-0 \-8 ]@ ^ &tid pos bin           8 v & ? ?$ ?( v0 1 '| E|  bam  !  ?x   Ql-m-s&jF{\(   g  g  g  g      \r ~  ).?up.hl.?ds.uXQ@?bc@?ls@u`RgQsRXhTgl ) R9 h )h gs h Xkey rPNinc ghk gdi g`  gl  ` h )! g  Xj gD"; t gHkey r`#val $inc gTk gPi gL:tmp rh g^ h )Hkey r@ret x gXinc ghk gdi g\  g`  gl!?$ h!$ Hb!@" x(?Tk)X" s-v`1k1g\Fp7h* = !=h=len=p?q?r?Hs?@str@QP$ C?cH?kIg]?E9 b]h!]`e?@u beh!e`%o? i!o?v!osvcq?v q?v q?v q?vretq?v q?v q?v q?v r?v r?v s?vintiwouttiv uow uow uv uv uv uw&"/tmpw"E !wbufwret?w"twtmpwl?w"b̞wr?v"aHi?vidx۠wtid?vbeg?vend?v ?vj wkgv     '( ?k) ?l*F?F)F?\)FsP+H?`retH?d+Ish*X?,Q)X?)XsfpZPh[Xb\`buf]QH+^?ij?@+j?Dseqkvh"r/t{Qt gg \  W     ?  ?  ?         ,,,,9,G?-   .V % : ; I$ > $ >   I&I : ;  : ; I8 : ;I8 : ; I !I/  : ; I8  : ;  : ; I : ;  : ; I 8  : ; I 8 : ;I< : ; I.: ; 'I@B: ; I.: ;'I@B: ;I4: ;I.: ; I@B.: ; '@B 4: ; I 4: ; I!: ; I" #4: ; I$ U%.?: ; 'I@B& : ; '!I/(.: ;'I@B): ;I*.?: ;'I@B+4: ;I,4: ; I?<-4: ;I?<.4: ;I?,(&: src/samtools/usr/lib/gcc/x86_64-linux-gnu/5/include/usr/include/x86_64-linux-gnu/bits/usr/include/x86_64-linux-gnu/sys/usr/includekstring.hkhash.hsam_view.cstddef.htypes.htypes.hstdio.hlibio.hstdint.hknetfile.hbgzf.hbam.hsam.hgetopt.h ./$&'YK=6/&"K=.ft=}.Jt<<E ff  . 2,.XX.tJqJ ) &2`7f.X2 %J'(,)<< .f_# . f ff.2,. 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Usage: bcftools view [options] [reg] Input/output options: -A keep all possible alternate alleles at variant sites -b output BCF instead of VCF -D FILE sequence dictionary for VCF->BCF conversion [null] -F PL generated by r921 or before (which generate old ordering) -G suppress all individual genotype information -l FILE list of sites (chr pos) or regions (BED) to output [all sites] -L calculate LD for adjacent sites -N skip sites where REF is not A/C/G/T -Q output the QCALL likelihood format -s FILE list of samples to use [all samples] -S input is VCF -u uncompressed BCF output (force -b) Consensus/variant calling options: -c SNP calling (force -e) -d FLOAT skip loci where less than FLOAT fraction of samples covered [0] -e likelihood based analyses -g call genotypes at variant sites (force -c) -i FLOAT indel-to-substitution ratio [%.4g] -I skip indels -p FLOAT variant if P(ref|D)BCF conversion please specify the sequence dictionary with -D [%s] fail to read the prior AFS. [%s] no records in the query region. X[%s] %ld sites processed. NEIR=%.3f;NEIF4=%.3f,%.3f,%.3f,%.3fQT %d %lld read_samplesbcfview??V-??Zd;_Zd;_@88@@0.++yDMbP?{Gz?9 ;int^^BpWPW^{-   G ;  pos0-3;7B 0s  W     ( 0 8 @ H P X (` .h Wp Wt ex 4 I 4 D !p ) * + , . /W 1J  ( ( . WsD{Z{` I Wfd W    W  I$ W4 W8 W< W@ H P X ` !h $p $xWY{ %e )fpr *fpw +YhX $J %W & ' 'x ,d 0W 1W 2  3( 40 5W8 6W< 7W@ 8ZH 9P : &`J ;fmt  @f` Bftid Cpos C D D  Estr Fref G alt G(flt G0 G8fmt G@ HWH HWLgi IfP JWX JW\ L@ N O O P Q  R S S txt S(ns T0sns T8 Vw X2 YWv Zfp [U \ _HXx  W Wac W    ( 0 8cil @cih Hcmp Phlrtp{] Slms(;/ @  bufWendW Wf% &W&Wn1&W&W &&W' (((0(8) @*H*P*X*`*h*pbed+xRG, h. /W0W1W2W 34W5 6(7W,8094:8;@<Hn1=WP>WT?X@`A @G/ pH/ mqIW IW$IW(dII,? {J .W p.Zhl.Wds. XS;W2 p;Zhs; `@Wb c@Wls@ `E EE fXksE h 1v ksE hW2 ksE XWTstr H@WPsiWlW6T ksE hWdstr XPL n1LWLn2LWHaL@N tO`vOhu1OPu2OXYW"YHaY@[[ W W W W   !\X!\`i]WT? jWbjajplimW!mlW {{[b{Xkey{ZPp}`q}hW8 b~pa~pr~~W~em~W~sS~!W~!W~fq~r~a? 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