From 338bc1fd411a57acfb99562279b5b6bf1a053ac3 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Mon, 4 Jan 2010 22:15:11 -0500
Subject: [PATCH] Added +1 to start reporting for GFF features.

---
 bin/closestBed                | Bin 90224 -> 90224 bytes
 bin/complementBed             | Bin 91456 -> 91456 bytes
 bin/coverageBed               | Bin 89904 -> 89904 bytes
 bin/fastaFromBed              | Bin 90760 -> 90760 bytes
 bin/genomeCoverageBed         | Bin 112440 -> 112440 bytes
 bin/intersectBed              | Bin 158536 -> 158536 bytes
 bin/linksBed                  | Bin 95360 -> 95360 bytes
 bin/maskFastaFromBed          | Bin 95264 -> 95264 bytes
 bin/mergeBed                  | Bin 98256 -> 98256 bytes
 bin/pairToBed                 | Bin 176872 -> 176872 bytes
 bin/pairToPair                | Bin 113728 -> 113728 bytes
 bin/shuffleBed                | Bin 104168 -> 104168 bytes
 bin/slopBed                   | Bin 95368 -> 95368 bytes
 bin/sortBed                   | Bin 94376 -> 94376 bytes
 bin/subtractBed               | Bin 90080 -> 90080 bytes
 bin/windowBed                 | Bin 94216 -> 94216 bytes
 obj/bedFile.o                 | Bin 76652 -> 76652 bytes
 src/utils/bedFile/bedFile.cpp |   6 +++---
 18 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/bin/closestBed b/bin/closestBed
index e94cc484f592158187dd08fabfa9014021dbfc07..b1d3412f3d06cb2188ee7c6794503c5c87435682 100755
GIT binary patch
delta 193
zcmexxfc3)x)(r`40yYNCZJz~wnKnNuUGmmjCv$TFTeGcpuM?w3w~%MIiHb+B?ebm*
z2Ezj{=C?91cr+hTh<1!Qc{q(<-i3hyL~fRIDP=^}u(2Dg;eRuB4f|Y|RZI@q+%);w
zKGn&;H=8rXaZNVa;=v@rIk|3&hUhyEptere1-lp-7#Lnp^ys|)BAava?ky8GM;~}<
M!#HEJ<6r$`0G57At^fc4

delta 390
zcmexxfc3)x)(r`40yQ6Gm$t4E`Cb|I{T%;{r9U<our=FicV6)57V_*iQSs=tUD3<H
zV0hrgf>s6wkLDu^(T*`E52x|VyD%{D%QrAEY?gB=Wkk`isT-_;p#_JAeXh$Ycz$~{
zALj6AJ;2|>z&JU5vl5Rgl9`j|?aQry?bEq7<NyEvEtg88J-VG0e7ZAU_;lu;@a;|m
z(y0eLdR>7y^n|bFQxAT(Lmu7L3Lf18p55jzqPZ9tntw2q_|yb?bjD8b=)7TgsUx(*
zqZ^1Dk906FFaSN_80#447=QAxM|W!i&=wEN2#HcxpU$5iowp3Xd2}8Rdm+gQ^gyTU
zhFy$69k2HT?J3__ydI>adn(9bKxN%~L3&@j=K!l*08u&Bqx1fY9I)oOAax#{hkd)v
XUs?j0X%jX-*q>m_IB&D#U;ShNbF`<1

diff --git a/bin/complementBed b/bin/complementBed
index c09cd465e028589621860700e1029c75410e0e8b..759abcca18129e392f0192665af5c365ede1fe4c 100755
GIT binary patch
delta 195
zcmX?biuJ%L)(r`40=ZnyKeo+lu40)b7d~a>*NdAA*piL4dz~0Px`jNuO;kL3ZS$uy
zFc=<qad`p*gGcibg=oi^lZVsz<y{yUK;-6smZglS8Y-uPH5m6}*D%j|Tl3@=)uzeU
z_Nz|TRx@X6;+mYI=D{S#IeDF$hUga#ptere1-lp-7#Lnp^ys|)qLXv-YqbfRy$}Ai
Oo^0^eWOL2mBk2J6bV`N*

delta 394
zcmX?biuJ%L)(r`40$v-NnC~nRZVYR?s@JsPE$`+6wq#@N&I=yhLZ00wDjvPI1=ATA
z3=h1xGJ%1?qxpzJv}4T4!)g5TE({F(@(m0OoBvssGNNdxnhMrn(vL&KJnL=EJik4f
z4|9059^h|bV4OT%Rf$Ix$;`=p`*Z7G`*g0&`2YWZ%cat2k8WoLpYDtoKApKIe7n<t
zbm{?*URNLvJ>hHl)PvvckVkj5f=9Q2XSex_dM*Zr<{u0tJ~e?Jov{-<I&T<W>Im)d
z=mz4(BOMG33_wpf#yZA1#-BXw(cPK=w8g_RLZZ~wr}L*r=Pko;9-YU-UdVF-J<#d8
zVHYD%$Lsw-d&)N!uLmjVo(ggpP+9k0klq(xIlw9xKvYik=)C`;3#@rANS#OLVc%}^
bmzF?g+Jwy)4pi7M&YNub)_8Nx-y`V&(}k$=

diff --git a/bin/coverageBed b/bin/coverageBed
index 0b0692ca1097bdf6f07e74841ef53dbb8ea46f21..89252ff065b9bf27f7620d8a4a4642e409fb7c94 100755
GIT binary patch
delta 193
zcmdn6k97kOC9nw`KK{$`V~+gc)dgMGkDCVm*<8TJY@yxj#OTp2<k@Ya;?ZlXKb3*O
z@W6}7eGCj9%|{fX9b--&PUDw%VPF7}o9Ee;GNNj*oDA0Rxd*!jJBMYBldo)Rnw)k>
zb#nD~bEY7!$y>I2F!69s{<mF2^brS8Tc_)SU5pG246i48bY6cE$vN42$Arzd52so(
L&e-hu_kAJ&PzX!j

delta 390
zcmdn6k97kOC9nxhVbA?}rRa5M=!tb!shdx(+FZcKY@ywG!J}Kqv)e?)qu178Dg%Sz
zffrNy7#KX7k0?Yt#+*Ey#xL)}z`!rxz`(G1o?R&;iUzC6U=3e-aA>e|Sk}n%+oSm~
zhezuH{uTzt$<Mbb@u(u1Ia%&dZvAVY&b1l;|Nn2fR2uEk?X2L_o$<n_GxvmVcN&mR
zJ>b#n3dEr&d@Y}P@Vg!I=&n}q=oawoHh<yI#lX<~gQ3KyCeWiZc7jLe4Z}+vp&cIG
zK-_qwgMono=n2PI$2iCMlZQRJTN8k`cvwbAl)CzK{`Ba)W%$jb^LW?`UQVC~I$byH
zVg%}Vy&q^#`Nrb)ASK;XK@I~d>)s2}`{FSNSmgqU%Bdcm_g_STHO~d9^XNS6+im{R
W639%OusPxI153tvn;rkYPXqu9OQ$FR

diff --git a/bin/fastaFromBed b/bin/fastaFromBed
index be388680a3e541caa9ffb03ff17fd4db3c7cff7f..445b657484712ff76a8f1acc3c031c95fe5ff092 100755
GIT binary patch
delta 133
zcmeA;%Gz<1bwdK1!2PXjigrJgD)qAF726zi`~KzvHfIa%UMEJ6ZXwTZ6BUnM+vAfM
z7z_`*u<d1F@Mu1w5bYRq@^BizybA*Zh}?Y7u9Oi~!^H_;4RgD(YG|%=*k0$r$fX1T
DFM2OK

delta 133
zcmeA;%Gz<1bwdK1fZkl~mIu~z1roQvjWqdiqI+`zo3n*>=LL^$A<u3T6^~xq6O$Mi
z3=h1p>t$f@Xg;D4?HF_Na2mh73j+hcd;<f+=6iOfj3^o|O#o|{*Nt66bDhKXItNBB
FB>->2FVFx0

diff --git a/bin/genomeCoverageBed b/bin/genomeCoverageBed
index cc39fb5ceb10d1772e10fa76cc5e3192ecd9acc6..760c6d01c442835ffacde3b2e17616a42626f19b 100755
GIT binary patch
delta 194
zcmdn-j%~*~whakv0zDoA3}q`M)vtZGiDEh|QoFf;O*m7#*NM@iTgbE9M8%`m_WCRa
z2Ezj{Hcnz-@Mu1w5bYRq@^BizybA*Zh}^s`zmySG!^0V14T2M~Yw#;{Yn@yY)HGS_
zyXs`=U~{GmT$4kBJ(&DBC(jGk5LMv>YU^}eu#1s_f#LN;kIw5au5(Vl9Xw%k_m8bE
Nj5D@7+A@Bx1OR35M!o<5

delta 194
zcmdn-j%~*~whakv0_&bsUcUB)?YREe&ffSdqTZVe*n~5+J1=;23wd^%sCe|+-k8O}
zV0hrgrb!G89?eG-q8(#S9!}$zcVS@Qmv3NT*t{;klo3V4qZwcgLKAUl@GEp{oowRN
zG+FGs>g3x_R!nEPCW||}F!^&%j&;@$RpkWg>vUbPi;;nW;q_FH&igNJa891(EVWtW
PhmI@byzP#*jNdB(BJ)Vo

diff --git a/bin/intersectBed b/bin/intersectBed
index 7fe601af6c118bdc8429fa4a0dff11ef10f66059..c789efb3f822f49b93965e8890a3c0694496396e 100755
GIT binary patch
delta 199
zcmX?cjq}7c&J77{0!RPvIwy1TougBZ&3m`Nwc?u#*n~Z_dz~0Px`jNuO;kL3ZT;05
z84M4+XqIMV@Mu1w5bYRq@^BizybA*Zh}^u+uaps0L!>HL!(&P88vFv(8YZV4ZJPY;
zg6d@MW9CfTW=wWD=E1aW+T^}t8lpYZ7#KV{T^H<PWME);J<+4{`U}hHlTRO;usQpZ
U>=VWr(*@Tus%~Gmjd9i%05Y~se*gdg

delta 396
zcmX?cjq}7c&J77{0&yDAQ~ZVX<#v57UlzFM|FX>mY{DMeofka1g*>}WR6KfZ1JoHA
z3=h0$k!ED@Xg;D4?HF_Na2mh73j+hcd;<f+=5>Chj3^qSRKXgaNaE1o7ogU_^V_5O
zFo#F$0sa;S#>wSJm3UN<%$&ULLT>$QpU$-z|NsAQxl|hM(e13@)1C3cr!)72Z+9Ay
zPCek!>k7o7CwwiRdhoj)^60Ks@aPus>^6U~c?JVR^ACm+pPE3A&e#baoi_|Gb%b_!
zbOUkYkq!n12B0S#V;$oh<4+#;=x$8_+TvjuAyMk;)A`e*^OoT^kIv&^FSbu(VDRX4
z-LQ)hsN?m1pgrXqi`RpcbWa6245+MoFG%l;UWm#C5S3FsI`6-*nhw%D7o^Uk^RREX
f`AbV6Gi}1=4;N=VVVpNza4n<i_I2ABXKeuheK@Jv

diff --git a/bin/linksBed b/bin/linksBed
index d8964988051cdc4fe281417da3e7ec93f59690d0..8ae801f233055dfc37cd965456470ce41f08684b 100755
GIT binary patch
delta 194
zcmZp8$=dLebwdK1z<2L;9A{?OC;gnxT&i}ed&%YkwqytGUMEJ6ZXwTZ6BUnMTk+Wp
z42B0@WKLpW@Mu1w5bYRq@^BizybA*Zh}`_ot&|Z}gW^oEhLaPpYnbQZ);jshp{B`c
z=Ts+GA2w%d;+nkWum_VF=j4BfHAHzhf!aD<7wlqWU|@JX(WCSFi%!nT)<-66zI{H`
NmT|^*M_xwzbO5hbNfQ77

delta 391
zcmZp8$=dLebwdK1z@>Q>25UY{eE8Lxja#H5<p1UZwqytG&I=yhLZ00wDjvPI60;c?
z3=h1>n#921(R@T9+A-$j;WU1E7X}7?`344t&Hvm=8BsJS%>-*WH35f)c^+=9Jik4f
z4|9059^h|bV4VE?kP?q7l9`j`&gIs>_UT-k@&Et-mP@749^K9gKHV8Fd^&Sa_;#lO
z>C^)ry{<qUdcxQ8sRzH?A&>5A1&?k4&u;S<^;`@L%|94Qd};zcI%6kzblxz$)Dha@
z(GA3nM>-f77=WH|jCG82j6ZqUqq{W$Xp4tsghZ*UPv=jM&Rd4xJUWkuy)fqldZ5#F
z!!Aakj@SEv_LOfdUJp{zJr(3IptA10AiXbmAu1O@R8IBiy#JyLEHoFS&ZG0NZ@2kN
XOCU3C!sdkY4{RCdZFl5lv`+^Bea57X

diff --git a/bin/maskFastaFromBed b/bin/maskFastaFromBed
index 83b1d0e4249e288c250108a4a8f14220648de49e..022968b91432ae6da5a3f887dd66be9a27864007 100755
GIT binary patch
delta 133
zcmZ4Rf_1?Q)(r`40ve7<>p!2*dOk%};bC>N^wiA-Y>S<=dz~0Px`jNuO;kL3ZI4f5
zU@$!JLUSSmgGcibg=oi^lZVsz<y{yUK;&jS&r(KI4Hu_?HFWl4)zEy;Yx_MfMkh@G
DPY^IN

delta 133
zcmZ4Rf_1?Q)(r`40{1@Oeg085=j*NO8Q*MX1~qRkU|Z~@-Fd;ITgbE9M8%`m_QW&>
z2Ezj{v?ekzcr+hTh<1!Qc{q(<-i3jIU%r8XVY8iQDI<!8OH;ray85weXujvQ{hk-2
GlO_NFgfq+l

diff --git a/bin/mergeBed b/bin/mergeBed
index 1e45c40b78841ba2bf27b6be426e758978c7c71b..b47e7ac5d71d9ce6568582b656a36d7560e6ff5d 100755
GIT binary patch
delta 199
zcmcccpY_6j)(r`40_!hN7TP5nSFiGmYx9RkT=zB?uo*{a_c}3pbPIWQo2Yp7+8&?G
zz+iab#mrs?29M?=3ek=+Cl9Cb%eyczfXL0~;z}7&HC&ts*6_0%yN0}kWet;At~E`b
z_E2^5>TBjq5nPj>T=QV!;hd~@T|@K{2T)t5>w;a33=9mfCwg>Ve-Y0)Is5vA&D@V|
Ttr%xapD4_zx;;;pF)0ZEn_Enz

delta 396
zcmcccpY_6j)(r`40^(dUHHT+ykdjQV+uLIy`)_jrn{kA8=LL^$A<u3T6^~xq6O$Pj
z3=h1R)yu%((R@T9+A-$j;WU1E7X}7?`344t&FA7u8BsJ`nh4hLs~d-gyo6;9Jik4f
z4|9059^h|bV4N&|O^HVp$;`=q4|D5Z`*g0&`2YWZ%cat2k8WoLpYDtoKApKIe7n<t
zbm{?*URNLvJ>hHl)PvvckVkj5f=9Q2XSex_P%Z|B<{u0tJ~e?Jov{-<I&T<W>Im)d
z=mz4(BOMG33_wpf#yZA1#-BXw(cPK=w8g_RLZZ~wr}L*r=Pko;9-YU-Uhr}PJ<#d8
zVHYD%$Lsw-d&)N!uLmjVo(ggpP+9k0klq)MIlw9xKvYik=)C_T0jzm0NS#OLVc%}^
dmzF?g+Jwy$9__GVoHu=<Fr(`BJXyx1BmhICr#Jur

diff --git a/bin/pairToBed b/bin/pairToBed
index bd19f8e101c232886d7a99e4388c700748516384..c8c5b1b6c2608e59bc9bcd156a1456188443dea3 100755
GIT binary patch
delta 196
zcmaFyl<UP)t_=xn0;isxuw1pEH(uJL_~9LslewD<*n-z;_c}3pbPIWQo2Yp7+CKlr
zz+iab#p)Lf3?9u#6rvqtP99F<mv>=c0Fj&DZ7yX*)$s8PSOfQS>>B#EZu6TwWm(ho
zV=RoSldYGVGx<%QT(aDQ$#3f9eakgORi*;<b-FIt#mK<G@Oq+0=k*sCr%wL8e8P5X
RHpZzR7-ww1_>EC~4*(+JP|yGX

delta 393
zcmaFyl<UP)t_=xn0<8+Ui48~Im&V`Jt9d`;)`ramY{6@_J1=;23wd^%sCe|+zWBz#
zV0hrgnimWV9?eG-q8(#S9!}$zcVS@Qmv3NT*!*sDDI<!8PhY?qc%I|X(6@D)AJ1=(
z=EEEwtq1s97#JrnU#7&Pie%>WIu^#<`qw_4Ycu};|KD<{G}@!vS;40}<AqOW?g`)S
zG$5UNz@yg{h(k~KT0ZsQcRS?KU9I5JE#TR0{=$1Y14Hu<h7zBeK#$JY2_Bs{3@>$r
zc6f9HapRE=1_lP8FC1eX;~e8p9`@*NO#s^BVHqJ&>gv<^)1&j2;Wv-Y<6$rSrviP@
z>AGPTBT&cd{Xl!lHx{o4De0aHau`rq_g;|R7pf4I3m__|dUW1@aS1Fm7o^Uk^RREX
a`AbV6Gi}251FVb!9~tLuzxa(&d=CKi6|ENl

diff --git a/bin/pairToPair b/bin/pairToPair
index 397f9f6d8a2e2430433fe9b6170024616bdb64c1..5aa200544bd1d177092fd91b38506f97761fa217 100755
GIT binary patch
delta 199
zcmX@`gYCc%whakv0)Ors+dY)=-X1Uhe0xQ3T*c-Bw&2y;y-tiC-9nz-CMq7iw(FA_
z7z_`*h>T)j@Mu1w5bYRq@^BizybA*Zh}`^cV<{u5hMkFE4Lc*SYv|j&&2RFQB~8<h
zF)^x6wq9z^#KAeaWT^+!686damTHJru><vWx-Qto$iTqxdZI_?^%wjclYcLru-%%4
S(bsc&f)k_3_C3CgEqMT_BuW<m

delta 398
zcmX@`gYCc%whakv0zO|>@pm4I_`|WgdNIFs$+67^Y{9FwJ1=;23wd^%sCe|+Zb)We
zFg)-gDvE)@qxpzJv}4T4!)g5TE({F(@(m0Oo8N6LWkk`iD-o<=R|F0XeVe!W@%;8^
zKFs0KdVs%$fpPNkB}zQ1NM=s2V`9v$f9=z`Hsk;Q|1FnFqdmHv6@0ogUift8p78BX
z1JbDnJbGP$IP`?C<x>xSw?iJ?)e0Wn0-oLGFIYJl7@B`Dl=##HdUVE4@aVi@c&Q__
z!=oFB8;^7_Ffagp;TY=}=NNzTut#@m0?-x@%Ls{5SD((G9-X%gzj<^X4|}nc9q5Bj
z*A2TEfjVCA2ijA<v3Na5N%vHc!+^@V_k#4ksD`Lq08u&Bqx1d?0S=Jnxgd2Oorit9
f&0ksqnQ0TYA7ExY;mJ5}dZH7f@%BBwj4gQpZwIHn

diff --git a/bin/shuffleBed b/bin/shuffleBed
index d990a9e0f33bf81f771f3c6aeafde765344f26c6..530338cbfa80d459368abf36a348ff0c00b08279 100755
GIT binary patch
delta 193
zcmaE{mhHt_whakv{6XuIm#h@sBEk8j^<Edlyv_M+OA@quoftj3g*>}WR6KfZ?WZv?
z7#?_$+{?h=(R@T9+A-$j;WU1E7X}6px!Eqglo3^f=M=Dp!`;|5+{<ulm@IOyY4Wm{
zs*`u$GiPezn*8OS2a_D<WV`zsqF*?G+B#hq>|$hKV0b;zqx1TUPR_~I_a|(Yey!@n
MIAgn`F5~h{09)%xI{*Lx

delta 192
zcmaE{mhHt_whakv{KCgy1XT3Y?cMoSw4Li-@aBBBB?;P{7d*O!JiAR)JbG;%rZF%W
z9(a+`%fR5#d_*DIG3MmqG=6y(1_pll1_p-BcIl;zC>p$`fHfTH#-ZU}hFimA70>3$
z%U`NYKJ97E$TgYW%Y{jvbF#0OhUixgptere1-lp-7#Lnp_2|6+qKk8Km)E4tGOtyf
N80T$w)MZ?r2>^iNM!*07

diff --git a/bin/slopBed b/bin/slopBed
index 4ab09549b1320598f56f7f089ecb61cddf9c6cbc..144e8fa0490931bd11d13cc3cb8f70364d076386 100755
GIT binary patch
delta 194
zcmeBp$=dOfbwdK1K-glIuT_by-_{kZX<AhDB7buM+hrT=UMEJ6ZXwTZ6BUnM+wF51
z7z_`*P@lrU;L&_UA=)wK<l!`ac^3u-5V<+exs(xA!@=2L4egV#Yv6MgYo9#DsA=-D
zGpduVjm??LxF(kvdoT%cPTps%A^L&?sIAj=!7fGy28P!YJvy(ysO6me+jzoe>2s>~
Nj5D@7@-n)o0|4?dMy~(>

delta 391
zcmeBp$=dOfbwdK10NXC6H9pfO#UA3Ga9~mYyS<wW*e=^>cV6)57V_*iQSs=t-7%Me
z!SKKfjVTNa9?eG-q8(#S9!}$zcVS@Qmv3NT*qrBF%7~)j&}^`Vj!8H)@VSb$^ZfQ`
zKFs0KdVs%$fpPM3BPAYHBr_++oyo0#?bEq7<NyEvEtg88J-VG0e7ZAU_;lu;@a;|m
z(y0eLdR>7y^n|bFQxAT(Lmu7L3Lf18p55jzin$mVntw2q_|yb?bjD8b=)7TgsUx(*
zqZ^1Dk906FFaSN_80#447=QAxM|W!i&=wEN2#HcxpU$5iowp3Xd2}8Rdm+pT^gyTU
zhFy$69k2HT?J3__ydI>adn(9bKxN%~L3&@j<N&K&08u&Bqx1fYI<V%sAax#{hkd)v
YUs?j0X%jXtIJ>}}ao%=EUPkwH0B#hdzyJUM

diff --git a/bin/sortBed b/bin/sortBed
index 8c5e57d897df5bd40a759f516e1fc5f4ea3d02b4..0902097a7ccc66ec2d2a6de6929963186a672581 100755
GIT binary patch
delta 199
zcmZ4SkafjF)(r`40<tCPt9P(ouUfC|y-=^v>iy;dw#Omby-tiC-9nz-CMq7iw&~3b
z42B0@oUCDB@Mu1w5bYRq@^BizybA*Zh}>KkUCM~6p|BCGL9-gW2D#X4`IDa<Y?@ql
zR&{dsA#<h(uE|FZc`ylaPUbtTA^L&?sIAj=!7fGy28P!YJvy(yNadXDeR#s=*XLsG
S7-vks$jYd?J&%{sDj5LwH%cx5

delta 396
zcmZ4SkafjF)(r`40@v;*SOxOb>^Ujvetz?Yj18L$*dB*ycV6)57V_*iQSs=t&1hy|
zFg)<$R1E`zNAnSdXvdh7htv4wT^Jbn<r^3nHrGX$GNNcGY6NT0s>Y!~F7{eJ&u@?B
z!yF#12l!hU7$<)}sKld+WaebOv$^%JeLB}>{Qv*I<x*+1N4K+rPj|)(pU&J9zTIg+
zI`x1@uPYFTp76DN>cQ`J$fLVj!J}Kiv)lYdC>H}m^ACm+pPE3A&e#baoi_|Gb%b_!
zbOUkYkq!n12B0S#V;$oh<4+#;=x$8_+TvjuAyMk;)A`e*^OoT^kIv&^FN8UP9_V!4
zu!|9><Mn=^J>?sV*MpRFPX##)sH}T0Nbif69AK3TAS$PNbl!iF2G%?mq|T%Buy42d
dOG_X#ZNlb)b2sc5=S{!J%BZ?MkC)LZ82~X#r=b7<

diff --git a/bin/subtractBed b/bin/subtractBed
index 4c1aa74f8248b8c67a03dc63a4aad1d205223aaf..771ddc5db0290918a386bd9694bcfbfacfbe00eb 100755
GIT binary patch
delta 197
zcmaE`pY_3h)(r`40<W8VzG*+;%zxVWJm|7mPS)lEHe(0vUMEJ6ZXwTZ6BUnM+wyJ(
z2Ezj{=C?91cr+hTh<1!Qc{q(<-i3hyL~cIkR?3K~p|KOJ;eRuB4S62RDkigRYnnXm
zpz7q++sv8bxF$c@=D{SyIazPJhUg0pptere1-lp-7#Lnp^ys|)B9(J;_Vx*zxewb~
QG0vDA_(gSd-ru4m06)b{9{>OV

delta 394
zcmaE`pY_3h)(r`40?S-x$~I?nw%Yr>xG>QvwRv*^o3Vp-=LL^$A<u3T6^~xqif#r5
z!vilCv@$SwG#^ojc8ocBIE`Q4g@J)zzJY;Z^EtOtMidQAonQ?NEjTpfc`U2o`R&ns
zn8Ty>0DlVu<7Dw|N<6AaW={4ym|Oqar*mz_|NsA6E|o@mbUQ2fbZ5Nq>C8Rh+nola
zQxACbx&m?N317>n9{g^HJi4nDJh}xuyUkxjb1^V9|6nNbsR{JxjGf@odBgBhM`(vf
zHxM@->0n@B0D8hP)-ld8{^Vhg?$!jLEgqH;5~Z#_oj*M~ZyA2`=sX_wLYNciflk*A
zyBL8wUhfCmQ@*iyJxEFSRFK1f%DVT0^uBn>0am#HqH?N7=lvIHV9j$u>O49R`*xeZ
bv;;EKCTyN?XonT!yvc!IR5$1SElL6azQ(4u

diff --git a/bin/windowBed b/bin/windowBed
index 37b7a59ff5ff18c88e40b386602942196af9323e..115af27552389a45ccec2429214e453816051bac 100755
GIT binary patch
delta 199
zcmeBpz}oSEbwdK1z<2YKO+hj3VKS^rOBye)OW9n&ChVZy>%{2ME#%p4qT<nO+di9t
z!SKL~pA#4uJerRvL_5ZuJe<Za@4~<UA~&ydD`iC0FmWbWLu5a84SpVMEt6diHch^E
zMs@P*gXT;TT$5D}c`ylaPR=`|A^L&?sIAj=!7fGy28P!YJvy(yNadWo`p|^U-sk?>
SG0vDik(p6-dmb<2tRw((&q=`m

delta 396
zcmeBpz}oSEbwdK1fcK9xx0n(<A4NapEIhGws^{hcHem<t&I=yhLZ00wDjvPI9kUr2
z3=h2cHGzS_qxpzJv}4T4!)g5TE({F(@(m0Oo7cIOGNNdhG!v{Lsvn02KM%GRp5GqL
zhdDf25Ae4zFis9XsKld+Wai|)Gr9GzeLB}>{Qv*I<x*+1N4K+rPj|)(pU&J9zTIg+
zI`x1@uPYFTp76DN>cQ`J$fLVj!J}Kiv)lYdC>H}m^ACm+pPE3A&e#baoi_|Gb%b_!
zbOUkYkq!n12B0S#V;$oh<4+#;=x$8_+TvjuAyMk;)A`e*^OoT^kIv&^FN8UP9_V!4
zu!|9><Mn=^J>?sV*MpRFPX##)sH}T0Nbif69AK3TAS$PNbl!iF2G%?mq|T%Buy42d
dOG_X#ZNlaYXDjR(=S`o;%&59OkC$;)5&$~FruqN?

diff --git a/obj/bedFile.o b/obj/bedFile.o
index 85aa0a13ddc82448e18a21890bba6876a9e1f9ec..bbac8da89135d56313d03290c2e5ccec30abf4e6 100644
GIT binary patch
delta 146
zcmaEJjpfZXmJNqFxO$x!J-UTFyG>Lk^RUaZr18tUY<|a4%7|5>kE^VE^Ovqf*3GH2
zi&ZAy*w--m!Di0ME4NB+t~wCM!)eaO!0?ZOLDyjN!!zle(^(+A37Z4Y{%4fD8OOlz
V7$|uRNG}7@bD(t4=FIcVF#zxhGT8tC

delta 339
zcmaEJjpfZXmJNqFm^v>^KE|QK$}iu*z_9rpM=2w!NFP^OH_va6=EEEwtq1s97#JtB
zcPsIzrt!<WFff2MP1ftqt$*#)xi;hf|NkwQN~1lxofUk#GhX;~=AQ8FP6N`Z2RwRR
zfjIPpujNw@ez!v&-PH;n-2$H7<}Vn4p!o+wiBC<SM`!E=kIoy0mpVc_Ji39n@kj?y
zHrg@9G1f88G5+LXkM7n4pe-Jj5fY`YKAk^3I&T?%^XNP-4mQT4({;lxMxc(@`+@e9
zZ!BIv*{DZJcB)6`eW?6gkQ+TZ5BqkTzqAB0(<W?gm>!`q`N3wT&A;~F<KZ-8V_^8l
uz@V!?`Qe##&S@+VUjOF6v;P?-Z^SV$JO)Z01=7oa^lT^{x;gVaa|{5VWr)52

diff --git a/src/utils/bedFile/bedFile.cpp b/src/utils/bedFile/bedFile.cpp
index 3a4a3bab..e5f2b329 100755
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -696,7 +696,7 @@ void BedFile::reportBedRangeTab(const BED &bed, int start, int end) {
 	}
 	else if (this->bedType == 9) {
 		printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\t", bed.chrom.c_str(), bed.otherFields[0].c_str(),
-														 bed.name.c_str(), start, end, 
+														 bed.name.c_str(), start+1, end, 
 														 bed.score.c_str(), bed.strand.c_str(),
 														 bed.otherFields[1].c_str(), bed.otherFields[2].c_str());
 
@@ -740,9 +740,9 @@ void BedFile::reportBedRangeNewLine(const BED &bed, int start, int end) {
 		}
 		printf("\n");
 	}
-	else if (this->bedType == 9) {
+	else if (this->bedType == 9) {	// add 1 to the start for GFF
 		printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\n", bed.chrom.c_str(), bed.otherFields[0].c_str(),
-														 bed.name.c_str(), start, end, 
+														 bed.name.c_str(), start+1, end, 
 														 bed.score.c_str(), bed.strand.c_str(),
 														 bed.otherFields[1].c_str(), bed.otherFields[2].c_str());
 
-- 
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