ELF>(@@AT1IUSH  HLx $ >  I  : ;  : ;I8 &I : ; : ; I8 I !I/  : ;  : ; I8  : ; .? : ; ' I@: ; I4: ; I4: ; I 4: ; I 4I4  1X Y 11X Y11X Y !I/.? : ;' I : ;I4: ; I? <  8int i ibi.. b# # # # #  #( #0 #8 #@ #H #P #X #` #h "b#p &b#t (p#x ,F# -T# .# 2# ;{# D# E# F# G# H-# Jb# L#  # # b#    4M(86 +$#L2,# -$# .$#bwt/# 1#( 3b# 4$#sa5# $   $6/K(- (#len)# *# gi+# ,# ,# -3 0#len1#amb2# 3V0= 6# 7# 8# 9# :# ;# < #(K=@a b#b b#q b#r b# t b#qr b#bw b#z b#is b#  b#$  b#(  #,  #0  #4  b#8  b#<  b b opt  Pbuf wbns cb#  ( ; H [ g s H     ( ; H [ g s ( ; H [ g s G( ; H [ g s ( ; H [ g s ( ; H [ g s =       !     ( ; H [ g s 3 ( ; H [ g s  ( ; H [ g s ( "; H [ g s    #   H b LiJJ Jb  FEE  ; Ib /usr/include/usr/include/sys/usr/include/bits/usr/lib/gcc/x86_64-redhat-linux/3.4.6/includebwtsw2_main.cstdlib.hbwtsw2.hbwt.hstdint.hbntseq.htypes.hstdio.hlibio.htypes.hstddef.hgetopt.h  2y+VT:Uq+q}U}9ea;VVVWVVVVVVVlqUUqqzq}qq}/:8 Options: -a INT score for a match [%d] -b INT mismatch penalty [%d] -q INT gap open penalty [%d] -r INT gap extension penalty [%d] -t INT number of threads [%d] -s INT size of a chunk of reads [%d] -w INT band width [%d] -m FLOAT mask level [%.2f] -T INT score threshold divided by a [%d] -s INT maximum seeding interval size [%d] -z INT Z-best [%d] -N INT # seeds to trigger reverse alignment [%d] -c FLOAT coefficient of length-threshold adjustment [%.1f] -H in SAM output, use hard clipping rather than soft -f FILE file to output results to instead of stdout Note: For long Illumina, 454 and Sanger reads, assembly contigs, fosmids and BACs, the default setting usually works well. For the current PacBio reads (end of 2010), '-b5 -q2 -r1 -z10' is recommended. One may also increase '-z' for better sensitivity. wx ,BFA Ix ,BFA Iww w w wUSsST\\VVsS5:PqvPO]US]TX]QUT U T Q(U#(T!(Q7EU@ET>EQTbU]bT[bQqUzTxQUTUTUTQ UTQ&4U/4T-4QCQULQTJQQ bwa_bwtsw2,l_pacbntseq_tn_holesatoi_shortbuf__pad3seq_len_IO_lock_t_IO_buf_end__off_t_IO_write_endunsigned intuint32_tFILE_flags2bwt_sizesa_intvhard_clipmask_level_old_offsetshort intchunk_sizetarget_offsetstrtod_pos__pad5_unused2_IO_save_endfloat_cur_columnn_threadslong long unsigned int_flagsbwtsw2_main.c_IO_backup_basestdoutn_seqs_filenoambsargcsize_t_vtable_offsetint64_t_IO_read_base_chain_IO_markerargvprimarycharbntamb1_tbntann1_t_IO_write_base_IO_read_ptrbwt_tcoefannslong long int__base_IO_buf_baseoffsetn_ambscnt_tableoptind__pad1__pad2__pad4seedt_seeds_nextyita__endptr_IO_save_basestrtol_IO_read_endannostdinlong int__nptr_markersname/home/pubseq/BioSw/bwa/bwa-0.5.9_sbuf_locklong unsigned int_IO_FILEint32_t_modebwa_bwtsw2unsigned char_IO_write_ptrbsw2opt_tbwtint_toptargn_sastderrfp_pacsigned charshort unsigned intatof__func__doubleGNU C 3.4.6 20060404 (Red Hat 3.4.6-8)__off64_tGCC: (GNU) 3.4.6 20060404 (Red Hat 3.4.6-8).symtab.strtab.shstrtab.rela.text.data.bss.debug_abbrev.rela.debug_info.rela.debug_line.rela.rodata.rodata.str1.8.rodata.str1.1.rela.debug_frame.rela.eh_frame.debug_loc.rela.debug_pubnames.rela.debug_aranges.debug_str.note.GNU-stack.comment @4` & , 1 D ?@AUPUfa U n2}2HY0`HZ*#!0ZK#0HZ00{#X'X'-'/ 3    %3;BI[biov~bwtsw2_main.c__func__.0bwa_bwtsw2bsw2_init_optsrand48getoptoptarg__strtol_internaloptindstderrfputcfwritefprintf__strtod_internalstdouterr_xreopen_corestrcpystrlenbwt_restore_bwtbwt_restore_sabns_restorebsw2_alnbns_destroybwt_destroyfree % /D KY^ k{  `   (- 4>C PJQ[ej q}    H h & +2A 8FM\ xahw |  h$3AP^m{   !"0?M"#$"#%"#$+7"?#\%cl&v'())*   % >) . |9 @ /G N bU x\ j q L|          x   7    # =2 TA !P @_ n L}    j }       ' M7 TG &W [g w   5  o    o% U9 T -b ~ <  e  . 5/ = L _ .   c b   r q  g  u      K $!) . w8 u= G V [  = ` H] O]    %-B "QY h Eqy  h ( (  0E 7#E8 :A ]PMXbg pTxb  j q   /  R " 7 uF N ] f n         $   G   $ j- < D 4S \ &d 4y   < Q  C Q < _. < N \ h zt      z ^ F  \ j Y$ $($0$8$@<H$P$X$`$h$px$$$$$$$$$$$$$$$$$ $($0$8@$H$P$Xj`Mh0px$$$H