From 27c154a2f04259c2e5d96974a631af7dc7f5ed49 Mon Sep 17 00:00:00 2001
From: Michael Cormier <35238534+mikecormier@users.noreply.github.com>
Date: Wed, 22 Jul 2020 12:38:56 -0600
Subject: [PATCH] Support for tsv files that are either formatted like VCF
 files or Bed Files (#2)

* Support for tsv files that are either formated like VCF files or Bed Files

* Add new functional tests
---
 .travis.yml                                |   1 +
 cmd/check-sort-order/main.go               |   4 +-
 functional-test.sh                         |  54 +++++++++++++++++++++
 test_files/test_bad.vcf_like.tsv.gz        | Bin 0 -> 3028 bytes
 test_files/test_bad.vcf_like.tsv.gz.tbi    | Bin 0 -> 443 bytes
 test_files/test_bed_like.tsv.gz            | Bin 0 -> 1696 bytes
 test_files/test_bed_like.tsv.gz.tbi        | Bin 0 -> 241 bytes
 test_files/test_file.bad_header.vcf.gz     | Bin 0 -> 7407 bytes
 test_files/test_file.bad_header.vcf.gz.tbi | Bin 0 -> 227 bytes
 test_files/test_file.bad_sort.bed.gz       | Bin 0 -> 790 bytes
 test_files/test_file.bad_sort.bed.gz.tbi   | Bin 0 -> 1535 bytes
 test_files/test_file.bed.gz                | Bin 0 -> 1040 bytes
 test_files/test_file.bed.gz.tbi            | Bin 0 -> 1871 bytes
 test_files/test_file.gtf.gz                | Bin 0 -> 2522 bytes
 test_files/test_file.gtf.gz.tbi            | Bin 0 -> 220 bytes
 test_files/test_file.vcf.gz                | Bin 0 -> 7960 bytes
 test_files/test_file.vcf.gz.tbi            | Bin 0 -> 226 bytes
 test_files/test_vcf_like.tsv.gz            | Bin 0 -> 1730 bytes
 test_files/test_vcf_like.tsv.gz.tbi        | Bin 0 -> 239 bytes
 test_genome_files/genome_sizes.genome      |   5 ++
 20 files changed, 63 insertions(+), 1 deletion(-)
 create mode 100755 functional-test.sh
 create mode 100755 test_files/test_bad.vcf_like.tsv.gz
 create mode 100755 test_files/test_bad.vcf_like.tsv.gz.tbi
 create mode 100755 test_files/test_bed_like.tsv.gz
 create mode 100755 test_files/test_bed_like.tsv.gz.tbi
 create mode 100755 test_files/test_file.bad_header.vcf.gz
 create mode 100755 test_files/test_file.bad_header.vcf.gz.tbi
 create mode 100755 test_files/test_file.bad_sort.bed.gz
 create mode 100755 test_files/test_file.bad_sort.bed.gz.tbi
 create mode 100755 test_files/test_file.bed.gz
 create mode 100755 test_files/test_file.bed.gz.tbi
 create mode 100755 test_files/test_file.gtf.gz
 create mode 100755 test_files/test_file.gtf.gz.tbi
 create mode 100755 test_files/test_file.vcf.gz
 create mode 100755 test_files/test_file.vcf.gz.tbi
 create mode 100755 test_files/test_vcf_like.tsv.gz
 create mode 100755 test_files/test_vcf_like.tsv.gz.tbi
 create mode 100755 test_genome_files/genome_sizes.genome

diff --git a/.travis.yml b/.travis.yml
index 5d64042..48bd90e 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -11,6 +11,7 @@ go:
   - 1.12.x
 
 script:
+    - ./functional-test.sh
     - cd cmd/check-sort-order
     - go test
 
diff --git a/cmd/check-sort-order/main.go b/cmd/check-sort-order/main.go
index ca824b1..41e9c50 100644
--- a/cmd/check-sort-order/main.go
+++ b/cmd/check-sort-order/main.go
@@ -58,7 +58,9 @@ func main() {
 
 	if strings.HasSuffix(args.Path, ".vcf.gz") {
 		checkVCF(args.Path, gf)
-	} else if strings.HasSuffix(args.Path, ".bed.gz") || strings.HasSuffix(strings.ToLower(args.Path), ".bedgraph.gz") {
+	} else if strings.HasSuffix(args.Path, ".bed.gz") || strings.HasSuffix(strings.ToLower(args.Path), ".bedgraph.gz") || strings.HasSuffix(strings.ToLower(args.Path), ".bedpe.gz"){
+		checkTab(args.Path, gf, get_vcf_chrom_start)
+    } else if strings.HasSuffix(strings.ToLower(args.Path), "tsv.gz"){
 		checkTab(args.Path, gf, get_vcf_chrom_start)
 	} else {
 		found := false
diff --git a/functional-test.sh b/functional-test.sh
new file mode 100755
index 0000000..62c4257
--- /dev/null
+++ b/functional-test.sh
@@ -0,0 +1,54 @@
+#!/bin/bash
+
+
+test -e ssshtest || wget -q https://raw.githubusercontent.com/ryanlayer/ssshtest/master/ssshtest
+
+. ssshtest
+
+set -o nounset
+
+go build -o ./check-sort-order cmd/check-sort-order/main.go 
+
+
+## Check vcf file
+run check_vcf_file ./check-sort-order --genome test_genome_files/genome_sizes.genome test_files/test_file.vcf.gz   
+assert_exit_code 0
+assert_no_stdout
+
+## check bed file
+run check_bed_file ./check-sort-order --genome test_genome_files/genome_sizes.genome test_files/test_file.bed.gz   
+assert_exit_code 0
+assert_no_stdout
+
+## check gtf file 
+run check_gtf_file ./check-sort-order --genome test_genome_files/genome_sizes.genome test_files/test_file.gtf.gz   
+assert_exit_code 0
+assert_no_stdout
+
+## Check bad sorted bed 
+run check_bad_sorted_bed_file ./check-sort-order --genome test_genome_files/genome_sizes.genome test_files/test_file.bad_sort.bed.gz  
+assert_exit_code 1
+assert_in_stderr "chromosomes not in specified sort order: 4, 1 at line 33"
+assert_in_stderr "use gsort (https://github.com/brentp/gsort/) to order according to the genome file"
+
+## check a vcf file with a bad header
+run check_bad_sorted_bed_file ./check-sort-order --genome test_genome_files/genome_sizes.genome test_files/test_file.bad_header.vcf.gz
+assert_exit_code 1
+assert_in_stderr "VCF header line '##fileformat=VCF... not found"
+
+## Check a tsv file that is formated like a vcf file
+run check_bad_sorted_bed_file ./check-sort-order --genome test_genome_files/genome_sizes.genome test_files/test_bed_like.tsv.gz
+assert_exit_code 0
+assert_no_stdout
+
+## Check a tsv file that is formated like a bed file
+run check_bad_sorted_bed_file ./check-sort-order --genome test_genome_files/genome_sizes.genome test_files/test_bed_like.tsv.gz
+assert_exit_code 0
+assert_no_stdout
+
+## Check a tsv file that is not formated correctly 
+run check_bad_sorted_bed_file ./check-sort-order --genome test_genome_files/genome_sizes.genome test_files/test_bad.vcf_like.tsv.gz
+assert_exit_code 1
+assert_in_stderr 'strconv.Atoi: parsing "A": invalid syntax'
+
+
diff --git a/test_files/test_bad.vcf_like.tsv.gz b/test_files/test_bad.vcf_like.tsv.gz
new file mode 100755
index 0000000000000000000000000000000000000000..03ad69a72a39d25c0fa3f2dcc3a0071c286fc407
GIT binary patch
literal 3028
zcmZ9OX*d*I8^`VYk_?iq<)N&PZ5U><BqmDMnb8PEAu44VOp!JF=pjoo_GPStF-;9a
zmQu(z_8t^rOm-%jAuqkx`{g|!{?~o3bDeXY|Ns7dxD}H4xY&-?0T0_nGY&SAATifE
z;0x&Zv;N7}dVPf(f0?p<|L6Vq`HYO}vxP6ZKh0a}5^AlMC&nlCSxKVe$4^I?=vQnw
z-f{2g*PRY;Vt;<>V0UGv)it~}PxRn%$lk`>`dl58H6O(IvA(!Onhw8U)EdrWZ0~&O
zpze&g#Vtm&wstobO~dx^<yl_)&Z4Qt`FU>g@~sv5GVeC<iLC81qo3>k%!;_NnWxPy
z7byFq#>kaX(&jhDmmYldet&-4noVlIC_e6B&j|9=;b3gh*bP2&Fdjx8W8W*j5u`dQ
zS@WCVJoRMq)5QZbK6U=Fr&0@RcRCVZBlmrsXNF)0w@6G}OE>J1i^NDJ`GJa#tN9PP
z8s0&@XK=}y(hIG7JL_g!F?0OK{O}?3MCQw`bj&%ag#Jo|^2w_da0fUQ9}LM3-^3z#
z7}Ue!%jG9S8{at|)YHWzWUf+(DYf&a3|+ii%sDw5jdpR&IY|dRPbCS_Xaz;so6mJ3
z{_KdiLObX9yTngTyKX$2gf;IBT0zs3E_p$(L}t83Ae~*sWYxLhldfT8{|r?3(GP6#
z0lL|U2WJK+1{-4izZf9(;}+&KBeAk`mR;#d>&qbq5Bo;0ol=o$tcB7Un9*qOooA9&
z&LX)1M1oN2dI4G%wAejzZDW=W^l8*&7*V>$xTcCi_c<nxVU#4LYXTwJXkRc=$1AsL
zj04;@;eCODys40Km_&kk$dSW|kz#ci<|cODlMxDgh4hFVMCP$=JOKO+fg*Fb25SK;
z4&?`O6P-nd$LM_`jRK+o^7B@^{Mu-7+r^M6_jXefw|-??T=5S%QP1?%DJ64Tia>Rq
zKGKHbW5-abLn};Ej>GXBRr;ULzLN~9%ES!cE*AETW^*2{@fS?dV5r$dg^&`ZT(4e7
z@)p&cgE~h;zd$X%7|5%&;Mbb9ajul-Xi9NgbHl4%b?$33UW1`@yRWn7R_CWTnB2qS
zhb9yHFq!PEVPu%rg;0Xtb7!7qRbL5gnM9)yoQD%NPo#6Ik%tKo{@JO?U)^;GP~Fg|
zPhqc;Cs3q1g(#o3)T4`2;6-H;D}j1;zOv)|?hoo4Jx?PSy$QL?cgG@#EN|l3AWf1m
zh*bYe4R7B27UCq+zEKdMq3>E~if@d+Znougg>&M*SU_z;tpG|A*1v9$)wOt|Bf9S`
z1hn`Q!;4i6ZT1)TOStF6u&P6Atyy+CpCL~VG7WV9CMh01J2?4E<!j>2;+CB8#CHQ+
z@vjlO^MDW0Z*dVnDhM<PL**;lr<jRLNabQV@=wX!8y1%8sIt^FqWOduYk*G3*F-T*
zcTUzX|HSZYbyHF_h7bj$Q?nBihm@YE32aoP@KPevPpWfc;7`dZD`$mkI0sRQWdS`=
zeZ?k>M)Apaxu^B$V3?ho??dbBQ^{>Xb`ODtpocJf3tHumo*XzgthH=uhmPPuhgny$
zQ3AF_uFaIv+6TFF!`C)FX-a<QmZ$3<gPMA%rE>ax5VHKefRnohl;G`fy{R#C(Ch5a
zn78$EHnvHFDfGs76~B$jl^pfA1uGtm^Nln)ejgeXtDGsJ!5PQPnOTsL9>Gf2S;v`$
zivQ{=w&qi@--uK{O>-E0mvF+xkeq8Rx;PA`5}dxngQ7N=qsz+L&DS(t`-fw1Hn+fZ
z<oh=a+d{&s;B%0!A3)EHdKVXEChh0c%dbFBu{v1m3q`Ax>*za9b|B`HVqPie3-{zV
zT2e9T79}Un=GA-TI3$bd(6Gh9QU%T<6xH>&+cizgVCkk{(#^tLt1b)NZv%<94+CR7
zR<{DbWiO;*9WYCpG6AZ8nMq@o*k2mVXRi{aHA>1I{T}vY&8>7=j>s%;#x4X-^N>0(
zf6$O~>BCI*SHLLm)!jxzD@o(?g4X>f)gSDh+0ylU)RWZ&n8Ni5<c{G1Vg9@A0=b{f
zRqlPGxuXovrV(cS^}KL$OIUKNv)6cTA*v*Jfy=3TL5O(vbNr3NT;xJ~7mm(zG#ebD
zE0@<^xY1?t#i*2E<f!bF9c!w@qngfD&YT$hpwq^GZT%JGNc%&h(gg)DlgX$BKnR-h
z(H1-;L=FrLWhXxj)OsZk#~wDLHUH-|+_guQNdOlRbCZ0z%i{L7nTmgvVaL@HtN|gv
z@TjnKiSanA+iGL3AtzTz?sdR=py<eMAFHe*I9N%Kr|%9e$r2ollOSb=T{rH~MjR35
z<%X&u(e<JDzC=d@JwHu7n=%KG-o<qn75^m~Ut4S0Ar(KP^!y&_NrfKiAr;fJ_gZ@F
zvBj(ZkfFiiu8X+GB|lB4UyK>h<?mV?vNX?4gJ&I|>!NmjF5mN}@!h$dr>*!QwLEpx
zhFRYk7+K<R?>jCGkv3(ZcV^W(&&{^Ug@uk2YArxD)sKHZ-PTZfa!C8&t{swEb~p8V
z8X&hS>HaGQC6*2?pPY4Bq2~ydR|m#$QjL?VMS2m|QI<J#gEfg@Z~dseyczpPlGFi8
zq~u!p7GN9n8<d&Bv~V$kf69w2jmeTduC7d|BN_(3ZswC#8ut}{bJKDF`TON=qi~Gi
z>&@sC52}U9Evm%{52!`FyN>p=1icP7sM^LpQ0)E?pSvc<M#?D*M|SOti%~UU!n5Oz
zVw&U0$%RGMtRL}rT3VHgtUaq`v_CZHWZuGi)cs3B1iHWZcsm_s8rYCvM*Vcs4Azh~
zAY^yJ`z5<|lZ4h-nIOtNN7{WpmgL?a&(LtaKE)^KEPX?I`IkAnLuVi}vNQQ#vxK`^
zZJoD+T$kwEk^6jn&TN+`(s6ybosf3wKhNGLKTFU+g(bLNuyTHV75}SCl%|&x(0*GO
zF?QyAO0|%EeidSd>dbbr*Gy>T7@Z3yoiM7NrUD(NBLB7oq9JE4&70rBG280OJ{I)Z
z7bw`VVsY4FH0wJ6HlvJ~0f+Y6gF&aduU7bEH-lPIp%po|l{SsV%4M|_V|L$bGdgCh
zb#11B(!DetT>J)aWp`71ItDiGlu_Q>zN|ZX9=M{cMYHNw0gsk&h!4NvO%r$`4LENl
zzrv<i&G|JqwqnGD7x#f=LKXN|SU?xHqI|5h%!48W@b<}+^Bv+89}d674Xc&~;GD#3
zoKkb(CL;B4;m;Ug#XBxoGR~dYsdns6UpDt_ucBw9&yy;!+#+<0ovt^@4)H+_rq*)W
z9$$fnSAW{@vg3b22BTG6tGFf+N(*hEpgzcWDy~4J4vdO0oMh)~<h&V(1q#NC1ucn~
zXbiA_<ThlBL`5VlLn{ak3c+-3BAp_yRvHnWo@j59|59~DRXT(RSQ=5-VDSSv>iPb|
zMKT&Mf29lU>k%aKHJXztMu^kY@A#!Eqbxe#{j}z~|K6)xdlFk+3aP+v5tfxF?6@yQ
zQXC5IL%55E8#!2~;r62w^-2=i1r}i$7{;hQ7C*jQOEhW{&x{Aa*e!i5N&u7WEh4*%
z=FOb8-n_pIlk>l1Wz-4zp!fcy#E8IFvB|Ho11339wa8b7e-d}pDvCmz7@xNt2oWt9
zkRK4OmsB%8YK5agkp`8ss8@OmmYcA~232xSo=C|qVCH966%Ak4xoKSVbIU)!%)KGM
z@Let=@r2#`(h36PSZWZ4w+L8wd7to}ZoH~;sfOpq`&(ettsUQmLSq((f1auJU6p0b
z=N2US69!oL?l0mIQGj@RFXf}V9PXDSo;$^s<{?a8yoAG?VEwA6`mSP(P9E`edl`{w
zKyEc;zbd-dEdr6rmJI^6dq@KZ(pn!q!_QG2IMsJ$ysTLk7MbF{{_B5CXFSnAZ~IEd
z<Xf6wf#QsC{b<R@|FLl;>q$UlnxBU4rf}oMoxX$4{_qz$@W7{mbdb#fZ>%_`Z}lM?
Ro5KIi?J{hff5!MD`42B5_E`V`

literal 0
HcmV?d00001

diff --git a/test_files/test_bad.vcf_like.tsv.gz.tbi b/test_files/test_bad.vcf_like.tsv.gz.tbi
new file mode 100755
index 0000000000000000000000000000000000000000..5321a9f8fba9b91e0cc69271b14932f45f0cf989
GIT binary patch
literal 443
zcmb2|=3rp}f&Xj_PR>jWT8wWm82TM{5MaHqky$j>ip#~Zlcj8mutTH40*?;q3C0Bi
z-kBDhyx$*6SgZ*z+_unXqWPsCo}25BPrLt4ZuMl3P+nW<-&u3cw&y*5xHEH>>*hU~
zi(`)%y-NIL<Zr(3_><$Qn_fSDzh}<=<8^cWjQ&UZe|uJI|NUg?#_ySb))|@4KI65$
z`uFV;{paSZQ|j_9&(~{&mv1~hLB(?t4UpWasu$;9cVrc8?%KHT+_v-U{GUIqk^TL(
zY9GwT<4^Tpeg3b&@SlM}9xbSf8QvZ><Yi#sU^b9h#J69iI&D#{Rblq+ZMl@9GFy?2
S#eeIzW7;XrzzmKp5CH)G*urN3

literal 0
HcmV?d00001

diff --git a/test_files/test_bed_like.tsv.gz b/test_files/test_bed_like.tsv.gz
new file mode 100755
index 0000000000000000000000000000000000000000..53195791fec54af7e9aeaabb470a2db41f51a3e9
GIT binary patch
literal 1696
zcmV;R24DFfiwFb&00000{{{d;LjnMU2ECh0Z`(K&h1Z(DF}p4TQ7=kMflY*<P9}{B
z7g-r;;&u!qb|;USzdsadiFPbLjzzTzSlL#;o_p@)r6?tTKK%W%eU5%@Un3H|tbRnB
z)ql(Tr>E7^Dtddl-@HD&tbe^N*N@T9)n?WIy}5s0iPL|sx107~E$^S#o9*)cL3}O&
z`lTSR-^6Ll?fzNI*Z1$QZ|k@B_M>QidBK;j58IcOI(%L|uJ1R?*VRAotIdP>UpGIt
z(c|~|^-U|_4-yqsT&XdMYVmb`J?C-zCrxvb()M*DUz4(E&-v>%yT~K<c^+MfFA~LP
zNt{H<S((U~kBAH+&Lok<l_GAo|E`{nnGM8T2qrlbpIMnan9f9wsUTu*ev!;!otlaH
z$#+a*WnzBbdg<hWDk+s?CNyGhUMiIp9Z;#6Yyu{qfY}6cGm~Qus$7VAPg<2E6-1gI
zs?<z20keUa3&HH>x?m1QUPHvIoyvSbWiH18oRtfqKrv%06N|i2%-GK4f!x$Y%*}I)
z%0iAbV9qtM9z!&!WD_uXFea5_39f8Bnn$Szvxb;lFypg4%Z@Uni48=oB{5E^RV9O%
zH;Osfk4iaKg2)0zu8B>s{AebY^Gg-ETrbQ_Ea%s|43z`SN{mEAz`@u*xM^Ur37GW+
zOdh0?T2?y}u*;o`>&>jqP*NPJ+-EX~`BgEAoyj5QC&9d~+iwG|fpF&nH?&-|tad~<
z80X^b%&@5KGwa|gF&h_NDzS9eyL1mR6FH`^n;#-KFhjYiiI|(8caz7ik_BU?a?HS1
zbRk-ME;CeFnGM8TC}wQe$sp#;ODBhz7lJvQ^-PXA967T@u9;Yd?siOKWrmL&%g@{r
zc`nBSyzDqqX<)KIk!xZTtTHvT4#q6xNWt!LDVRme%!!rRK+J_;nlhxB9AaK5oy5+p
zA?BrI=0$asbt=aaoI!p>OyjkRd(cbG#B$CRGs&$?Ea!8J&Qgw5KsPmURK^V|vB<Af
z<Y{JQvS2#pR)EAOtd-O_D>V~c)2YmQZe^nVy=4|vew1}hM6YI~%4DF&5xE~A<b*Yy
zn(BRziLU9?w5IPd(G}Q7XP^ubH72l|mfGB7hF8hP5DhBpV3Ermfw-}RT_?;$M=E7U
zvNIcqxlqi4TA3VT&IHpPI~&8?%eveT5Om)%6A!Lr<XJkPQZum(eO1gnu`+q^$T2T(
zl*++=BzFV^eSBljxn?$jBG<%lm8qF^Fs9rQh}&OS<n7s&A#zQuA>v#R+ng6xl^kNS
z9rG}9ac?CqNL5g=4s}Q5aIcYP;=9^o7bO+fMEsm55`81S#Cz>y%QTgWD;IrVc^S92
z?L*Spr1WM|`kpf)qsc)|hv+m;B)we?%lMd1`lAHXek)EE?@2mI4B8LrHA25t^nTt{
zYTkITUA{;*jrF4z;fs|G)cQDA+;q?tj<COV%0+kZQqIPC4$x2V#h-pkE&9(Rw=<1$
zMpTUK=Wb^>LjTs$V?t57+Zm6VN&2Jo!<yuzU-k4nMd@y5u6k#(%HYf)9qM0SI_+gv
zcxi|F08EGGD({?0iqgv&Xg2Xqds60J+M6ikx?yAoSU1eo=*%cw>rj6j<9UEp$z179
z&%boFSSFdF7SsMHL+Ku?l9?W2RXU_YvvjU!sh=}YJ<fH-6kgg#Ufnt9VS9j)9iRu8
z+2iMtIiHhOi`#LyTG*tu$O3EEM<1U7JLv6gZSh{~JIUmJpm5QFthP5hMOOEI{(*k1
zm_s&0*fYfzz9{9?rJNzY%sO9^!p|3=Vosnph%<}cnX2@1rbg(O9i61H7rjB8S#-{%
zBtz@boz)9P@9VL!*JF(+A2pMlbWnMNxZ>e?-X9fchq>$MRNVtc=x$$NI@Dw4{Y;{!
z9%H1totgJtp!D-SY{eY1p$@}3U*f#<@&&3#*7*__e!f5*2BwGYFy@SoUro*P$jQFz
zGD_nZt#r5N9+h77M>Ke)AF`qD<*`y9(%HCb@u#0sFAh3XF&@`nhxF!m(I?0%)L~$H
zJt;kG|1!_h@%_tO>nHSpBUfmDRAP4<n&?wY|M05-9$=T<7`Q<cHwtXdqnYi<W22r3
z<d!@d*=|EX-5k;VN$K`7n<1iamFV`z!%DB>V~FfqCA<H98S0|fNTI;m>q(udCv}De
qapr%@7BJ~<K>z?BiwFb&00000{{{d;LjnLB00RI3000000000)+D8BY

literal 0
HcmV?d00001

diff --git a/test_files/test_bed_like.tsv.gz.tbi b/test_files/test_bed_like.tsv.gz.tbi
new file mode 100755
index 0000000000000000000000000000000000000000..5f7f996d5806e0c941309163c7788861e5d34a01
GIT binary patch
literal 241
zcmb2|=3rp}f&Xj_PR>jWR~X)&-OGE(frl-ieLv%i7ZWsAPMFcary}Lzd{)cH;iQa?
z`*BuvCC|eQHs05)YoA-sFaMn-5*hmPmyO=utWBOTeRJ%87S1z1|LomXAO7z(=4aMl
zT%Vc#Z2H&w{?d2Z|GRgbU9>rWM*O1q<wwigR6Hk934Mysea#yzT=li$Gy{V?nx~{0
Jn8AJo5dc^BS{eWV

literal 0
HcmV?d00001

diff --git a/test_files/test_file.bad_header.vcf.gz b/test_files/test_file.bad_header.vcf.gz
new file mode 100755
index 0000000000000000000000000000000000000000..9a4fe08cd14c98961ada93ce5e796d892f682206
GIT binary patch
literal 7407
zcmV<L91!CliwFb&00000{{{d;LjnM-8r)l3bK5o+epY@3r+I02REHoyf^^n9qsofx
ziK3{M;><p2XbG~pOOYx`CH0Jd{2mb0g(7&BrDmH>6PrB1xqat?3*Wx|a66dv?ymlM
zdwn(PjK}S37R~}^6*<0l^;5@nm4)L*EC`jA9foZF)4$%leG8A+wH>i5O+`f2R12Qn
z4nKSrv-s}w>WO*N-$(7?dilVDE7YDmuh`W%3LNh-&Efa8?K+ViIp3JF3fSD4@#o6V
zzQ+`Q0gwC#`@wxy=JwKl<fE09ABIl)(F60GM^EtsW$pdf^S^t)T*Pu_Wg6aBkO?SQ
z;LL1S`DVLorhI>LW>1O}D$x^5ByvFLXZYQY6k7?`4`Jj)>sWFi+X)u>Vv11lm>sY{
zK??k%EPeQE=6efg&b$azNi=73CGtTVWzJj%MtA&mc%aGrVLTj75jHn^s6vkqu6>}z
zy&X8V7lq2tjyH4Ha}Y>@v7usnbH(w1Mfi*2ELVQO`7Q!~sl=1Z_;p>!gZZZ5Z;Ujo
zR%Z@AoWbDOnjtvJS-_9pjLA5^OW33(=zbo5y6sL4TFP|nF9Aq1Wx3{n^1V=5`0H3%
z<!QaNJtgK0P>xx0XNtMGPyfSa(E(-vFI|7mO4)7*x$A9ktLxeiez1XbJhO0X1TF=H
z&OwBTJAq3OFjvU><g7T!cg8&Bk$HXu%wkt@+=|~edW2~~d*jj6(A9FMOn~2`4~_t*
zaNfh4!Ed)p|FhEj(_b=W%>Gz2Z^m&lO2p=v_m#O5&irp6y9a-}TskIDv}Cg<+jGKY
z$k7au^Z+pc!(q%5;5}+9?izmOqz|s|&-qM#!1Y%io|SONFA1!Ofr>LfhHAhbV;3f}
z3I}q-fTZ>;fFuC3flwi9D-f(t?(?r(OM%h+)jBb3+E_RJPuIVWzWg=-NO3gd>QIhR
zvo{{%JhDR;f#FsW<C7?S#x%drgX`(1FN4W#XE5l&pbF{dbKpSs05{E^f=kGDmjPQ`
z+HRzPv0~d~Iox;dZac%tX7Y<8Cx>_bvITEj&b$Q#Eg)$90hzibib2cq7XBO5GAvB=
z77ro|Aq$zUZmZL}fd95J`+hR+T#bkK@9%q8;j`y^&r8T@({IA2FY3$kZrFM04aXCe
z|G`*Cn7#*-kJ#!;eYwrNx?>Ce>Ne)CYdB^_G{YdI)o)Gmxi1|kUtY*6^X_I|jh#gV
zFZPl%OmaxHDK$X2DPGe}L3lxV`t*f9*o=jzIwcyY(|JX8KIN$s`7VQO#pW;Sg<%!y
zlT_ZFKI(<3=c#m`sAR<oAWX1fso<gRD=O8gqLixFRm#wDiB?1vTIq(W6QdY;4RC*7
z!rn-Xs#}(&>#uCoQMpl3kwrx}CJBv1hXLqd8VFm$hQv^jiot~4qfDq<rm4~PdKE?i
zvzJp|rS^!U0P1F(26saY)zVbjuHqk}sfJO75(tr{R-(kzGH@+{F+r-K?>sfhsGs(p
zkUI4&kuUu$mSp3eQS2T7w!j$11|pDVix6I4hgUYbFlBZ3l*WWGr#vQPRuuxsEq#}n
zwy;L17nYeBu~#OzZ#0rrU5)ZgbX46-kW<|ur}1`O9~MW!SmLj-#9!mgv}L8iLV3;^
zC(hAD5yu8WhIwRDk_cL!!-bON^9fL%#)TUstz2iurlNu0BVGm0(hi=dGA4)d_EqAm
zuM(er&8U`&!DL!VQ-FwsL#k^qB<xZ%pd##Sir|GxO$jIY>n)$0(SplCp0<$a1q{<L
zb>qlnP&GeR#an}_oZziuXzU;}mOw$4271NmBAHeKnXD@g5J71PWcCRXK2pf2mV}f1
z^_GvckWh)PIc%~$07aTER(Avus*~acNgWpxYEsRrg$knU7OgiV(YOMZD*~=wY|LRF
zvW9*KX#SXyFZFDTijRkUrK{8n6-(wjAkie#ACRC7w~}&6iHz|Uf><v^dg^t;FhOW9
zMkpbKitI;C)zn@Qp@va6ZxN8jK#knqBoh8ASl6>6v548OpBi>?a3g`wjRZ3{d2z6x
ze{~|6EssE&;&r_!0`^j?Rs?&Pyg0#=JlNkQu;+z-1N)M-^QmDkeEf<qi>>tog;9Oj
zi%f6~>`PYcTS$$nz#f-1E?6&#3v5(@y@ZRbCJ@Uk2#zx38)E5;kfss~(tSq;eFr=m
z@C|Ps0E@t0GB{sZL}lPyFgscYY|32UdyG#HfHFCzVAJGnc2xQN35aUW-w1kfXLb7M
z5m8@B_1M9+RgXuVxI=7Q<x@+3cw*7bevAnX$&nlP&D+P*+pAixZ{oeCIkSnwD;BGq
zZai6VRqD{CU5F-`tzMf_aqA)5N3@S>QVyDLT}3<Co3FP;+_-H#4KizC<}?jOgHUb0
z8ri{qAi>8VqwxV<?jlq&S<ZX;@-xFkhIwStB2dF&hJ=m$b-Mo;Z!n+qABJubou7;J
zkIMDc)@bL#OoN14tNTAoaXu3CcM|;EWn7VZmd^DJLBE~2FepmTjx0;UQcfwW4yBZm
zO=wCe6=xoB$`6R(3)22;wB_e(n+1$(0;d6{o3!UxqbebFg`?D>wYx|YQ@Cf>sP(L}
z$`UE5?kekyef_ByG}|i>@AqzPU7<@JLZ*7zeb?>E0tz-ZyWL3_{&e7nPPgBm^gI22
zhd+S-C;fi615aWKpo1Se(y|n1mL&X6A07>sB<Bkc5xeII4-tr`UJD7tCr7Vy-}8gL
z5k)7j37o~{zv&jhCFpnHwrAzT-GhjUg0(lRyafPP4S7sXH`vW95~Xw^kL>DvUsC=0
z8S>4=i@|7o)9+o6Mqh8>ubUeYrY0hLVM_RR)TFHLH3*1Pm&!(Aa0~=axC>M{j~`Wy
z&XH|I{%n*C8>EiYXSKM9Y#YaH1vHU<Ie9mkywO@j2S19)A}Y01T70v(o)}z`3QI1H
z8iv*OW_x(vBlc!#Fd0bIjCwI4#_ST(@Q`_hqg+8(wkE(@W=P_OkFl|JO-t^RVok$Z
z@lH;ai(<ld4cu}@bNBLW(i1iz$-Np?gR=&$7=S+vni|+#e%rnXfT%VAQ@6xZ#vTh}
zo7P^mn@3(^`oDnRb)K<Pcg%_`z1yipR-SqLv3U(coKHa3Cj5hqBI};q1ntvh>!RS6
zSXZ+unHQ^iv3V)p><PjhJjxFx`^TgANA!byXE;Aq)XNhn&&nT!m1**^55OH+0O7xV
zL(n~^k>f-RpJE6oQw>o=E#BQexh2k$DXMl|#YInc^$q3P`lGNl5tn$duE7D?U!9dt
zS5>7~bn~;at`%8&chIAmdFJg4^U|cJfR8-kTc6j-%0G5baZ?G)^%BP6kwVJS{}z_s
zbZ=ONrKIti2f?ugtFJiDXzOvFO?V>JkZC5Lfj~=3;Op4pOCe$8ucnW-<M9YM+^0}6
zd{R<fH4GmGw83E0WJ{0znbJ{CUnBt54Wz5>QW<G6iH_h(c6BvWi;_BO#Pq{Y*YfEP
zWP!~KY_;)}JDg3wOzz4^i<Q?2F0l_7P&LX-2p8@v+lOML*0GPEue-?u`&QLOGEA(Y
zIxge%yMX#f2J)$A2@11x^x&Dm*#TYbq4YE1lK+)=b-Q)jNcg(@C;>Lm|IcNR#<dYQ
zh#SL3t`-5--7T=2VBPfnml8=GQT)gmQsg;udn-}okeZoqW;h&f`xF1*lyL|Ix$p~e
zUiQwb1F{Lv0ePCCsrKqSS}SlAD@$=q!je$8Bot&Qj6i6CfI@-CLTf1tEXeAlTvZA0
zW^d+>q9m_G(o~$`$1*$v`KJyj=9~qbm?zLEopdqXwd8#U2{Z3!)4sel=%E*}$lJBW
zbEdbUW%b%xTJxFK2iMm8?QeV96JO|a<xFW>T@H|@+cSiohNp?1m6HlJLt+%V*vk4q
z=Q4K~d|02@SXKcSa2ddQ;Fb+o7J78OI^^ifI`Kwd4&MJb>-Vux>ByB>nX&e7*hFcQ
zY$6(SVxBGC%9@E8f~~=3{)!qxe#(X0s3GL1TquZ~#q=px)yEAnf0`HRqX<(&Wd;8@
z0g*#xwb0^LZ2mNd&7nPt2&&YlOlu)tOmKC#1te~a<`TA6)vy-OyRoFtY^R~*!J47{
zEiMo;0P0)?La?1-9;t_>%IgAQsypGsWlGdwn#4do-b-$fVdFRyq-TA4Js<;RwNcHr
zAR41EfX^;4S}t?<4A~oj+Db&XJGJE{0=Y$6v!N}*GpmMS%HZO{RW_T1t82K>o!Xa;
z1CrEU8=G1gN##>Jw-4kTK~Xt`v)h!<m=`5ONh(Fg8XJk|c6C{H!P%E%U$ntTiTZNN
zlh10T;etn6m#%lEv@Tq?(<<5gR%-E2mK1E-DJ}fT`URT;O4D+~d>cTpQ68xT)VsEZ
zm#Mf%kkfM2F@T`nmtexaIrQ7AV70Xp_-Jkq7Gw1qEyW7d&_b-fuE9Du#s(0N*1$u#
zSyZa2tOZbb`^LoEvTVkp9+CoX7<QgRBk*-upEJS`g(Rs1zj03Kv7l*S6^&6+6=g1R
z@hlxahHYiU8D57nlq5_uZ9F#MA|QnzjKEd?QyN?$fX`$`04@cWBp{P`YQte5o|2Gn
zBX%6%5|HV~V**iaObkI(3heC#SOc!eeXDf>!yxK(6ni&5CH;qzXNk<oJW=(7&*FW}
z=0P^t&x@UT5rd0wQ6QVwWJwrhU~Z2@8MJI`dG-OKETtG=J^}6>P@C&#S{bgMEz0@M
zVifb4*3x&@YTMrq+h;DoZ5lwa0cR*a>S};};08?0IRwJw7KL!VLkzwlJeXU0aZg+%
z1s20my~@ViZU76h`Wl%gj@LHcTb&P1(oD>KXJT&CR82$V8fDY|=ZID_J;gX(EfrK=
zU7g8wh;jhKVzF_iRqDw0dE9Ph6y+SAY+C<($YqXlZDN@z2_csan<_>~Kr@7J0Iv=R
zpU5O?I!EGR59SgC+BEEkASws;r^SGfyAu@~uoP^-_QQP$rXm;H0&Ej<OF^zWuwVA=
zK%8>UWGQp?RMd`C6h2Eea42OiO@>P=X>M>-no?ml8hdVXyO2M(kho>KcnI4I4Ljl$
zXTKcE8su&V1R*^vJFHZT`AqBB_ZDB9&m>oF+9~b+-r|RCf6_O4Z~bR`++kA|Sx$!t
zOzVjm?<qiSN-$+3G7YA0bkKpdaE7)K=+`A!rFDZ5teAHWgNH`7masm>`cjHzIoYsW
zj$kQQxI2KAT)l3=I<7h&z$&`z4Lj=IfF<-$J~&BJ%eOudw6YjlQBa~PlUfYiy*#c8
zj`Szfnk`X*KyHK}257m^mDkv~INS&2K_y13%(i7-V<KyO<}4P-Y~N#x0iiiUZe&>?
z>i}92z&bz{h|5x8TMQ%|Q)o+>9JE0ImLkX=AZ?a#t0&T82!dq`cPV>=FbODw!fz4~
z)=H?Y!?zgfAEt|tJ5{nrT)R!&iOdDEwicA|qWZEat-nRV!ZGwrt0<?#fzxKJM$S1D
zaav_$L?0`0TW-M_SNx5l=1jfsh5={n$W<|)$?2FGJCbzcnIdzOu``pj8Dk!vC^ffG
z;?gdfDwpUlBpUj!1@sytRDgJ+L1WE?&ZN<EalF=3!LOHztR%Dp({OaIC*dM(p2Bib
zff8U@39+h$)~ZrgDq;$dT(8subU|gq)CjQ>d<%H(7I4rlV4GXOh_`@$Zmr>g1P>*k
z#3g`GLK{j#2TBPH9iZN21UV(xBfVbHTql}YqUn)&kHnJFDtFQQx~N1%|EHa0iRBoq
za$<7!oId4j87<Y4vFMBiaMnHh^FPR?F&tM|&I@l|SE(87BVe76fYUw#zWunJ*M@=G
zqE&lBO+6G-(a^UEYB$YG9pKjmK|`(|b17pi9o9+iU_%3h0jJ8RVMPs(wxDZ3$*BQS
zo9oXzWYer0lz><lEI{Nj+#Wd%^44O)vO~5RGB918t7+iZ2z)AQ3QKihCF(lMSy*=M
z&I;n0m1H`ziY+^G!H=Qhn40J$=~sZUuB^o}o-HhN1-R}Cu=$lWyd~)+AOpX(jW@sh
z=9h54<!PxGhioJ29j}4chUj;E4P+b5z-L%4_hc#AuErCLQzaPF;ar$&a}3$KoXQGQ
zMJM6DxBiUrY+=TGz`yr^ukHb--dn@t(qa{$Weudo2nh33>(F$1%7SRJ-Ay2*gGdKe
zJgh>Y71XlpTQE(!rJgO_Qcs#}xy+r>=h}gMqZCJ7NW~#`dy2L{Y{ZspQOkdEaZSUs
z>+{6APKx6Ju-*e;+y{&F%`?S}4}k3+tl`N!nV<;|6^GHF15~C_8<dX2NhQXeua>=F
zzP9WI^R;CVY+i2-0^_w;1GM8{&1Rzknr3A>l>P|7#X<I^NH$YnrM9#rFE~O>AS49B
zP75njAtn%tQp2O|9mLN@10>$g-D9Ld);mbhHZg`kD#o}lLrx_&I&6uwM^^x{gM!A2
z)TL<GB-VYW#kw0sIcLJ%_txN6k=~e!dFoSN;cdAXQN{Aqr@r3h4~ptNvm%QtH!45%
z&R9n9qh>5W_4KYI^bx(QPxI>UxMGv?Q{SShEsU7nHzC<qmUNh9*|lzXWpU!>nNlyW
ztQ9uf8G*n%r5f6`YUuVx0+~i^V6Zzcqa*{|z%7AX>VzHh4~yk<_X~(yl&~!hh;kJn
zhlV;J*71HJ-1WVj1a-?3Oi^L9RFflHo(y@iPhZGkSnrab!Wd+qV0%!g3RQ}%5~WeZ
z#h7nWY#JmJKCVjP3MoH8H~;*+Dk{IKpmMc9?$^T1MD7>L5tFONxUvAo1o_fVX%nms
zUc&&sSD}&d#1>_v&@H{f-6B5;UNO+4Y#OppZ!}>u`n(8AVcaW)(aCsXGfWNqcaXkJ
z`AMn1n3hxGbb>H-2rmL%c=Urc9rKyy`VW9>KLGyxU=2^07NjyDOb<%gL@5(%5|pNZ
ziEVUC-!6gK(yM*UK0P{RD4}UV^=SquZnUOY?!+7geS1xdV{G3iHgMS9Mdn~du&N+D
z4wz-c^*Df6<53l_;m&)g_3_%yuJQIldK}!{iJ+@z{jSD1f?3in7i~nf^t&1(+j$x-
zmuMTm=vB^QQ&mk@3C)pU$Kr)-Erx9cUQi>187(l`0VOP;WCxVQ023u(Qbg}aXK$%=
z_RgQrWNt{1S%-MXf=Ybstdv1UZj(R1XkTs<%6bgQt1?m)-YapRt}0u^eL7V37C9Ba
z2`+p7E+Vs&)c^YY<-bqA|6BZ3ia~#U`ttpc=cj)>{pZ`)e|?$07cGB(`rjW<Uq!4}
zy|urh`&TOw*uVaY?qB_g!2Zt?T@77R^%divN!AVRUwy^sU-Euv|LQ9a{WCxZ(?5Te
zO_zs~Bg05aNdK;dRAF*e_f<do9sgvWY~VI~wiQeU+kv5jtYVC>A=4)2jrA9dXA2J8
zSc_nOtI_6WJGlUBJ_s@!l%wxD<>^WhqM*ODGLdLQ9tQTvmVQIN0dpn$^zTEAFjPs;
zXdNt+CldNz*MJoV=o|kvCtOvKRU#6~In(I~%n!Ppg4>$$cYsCj0E^vOYhpZGnD!1Z
z-JLZ&5i2BOeY~juj%`NP#s#S;dSp+NE&W2>BmV%lY*7X{-KSSk^iCH*ZbObktE`K@
zAG>;Q!a|<l8&@}6P(~%Q1lG?vLtquh4R^-_eVGadSfhFjuEarXG5~TM=M!Ndps@Gh
zu^W%J3Gfj><cK3O@oVJeTiXd{#^E^h-O5kji|2~|C}zE&h$Y_oJBz!{R2(NMy#{P{
z4LI`}@Y^+DvTJK7B&A@`ja7~^?mbPAq{8AW{xoDPs<r<paEJC29ItIr?fgf9JL{bB
z7EkpJgVU*>X~#ZcUB^p{V4%r-2v<9yW3ds{N5F-Tfb|{$zdZsbd$fikkNfO5i}79=
z>8ASx722UCdpD~^;!C$=Th@MSy>-g>FIv835vS=)&)Dug4*b%b)eDR29y2?5qdk@X
z?DWwQ6dMH!5sEfQkU~Rf=-{j|h;<4UB5~=5(jI9l{ILboWd%rtZ_Rz|U;fto(AJ`Q
ztE%19R0UPLNgh4;=eMulo>#o#J9*FwaOanYRjp&jDMnF#Anwa*9N5OKY8^99)rmU9
zaTNA-H}EN(TZdGoYDXdUQOjP7`h0xSRO=wpgbCX>6Q_!DF)~hDi%O?W=fA5fj3Bo1
zRqYw&yY$~?w3M71#(!*z1G!sCE4%kF>6V=N+t=^U?2}9K8yK2VOKd)y7xPq>MDmSH
z@vDcXX$ULiAnO$Mk4e;43zq$FF(?V*`8X+s8;1+e+*my0kJ>LEy57r9aJ;Mo{hVHx
zF7|zp?5k>Hh_f$U(eFGMe>N64gdjz#_e+bZWP*i#-vI7;b4K=EpGODmTh|2tw*85J
zyCi2ZBL8c0>B#y2k0C)RAp0|5pU>I(7v}<i9&y9L#ne}lsry3N6n!I<ve%}#sI{0~
zfoHWxGb`{Y(K#{pJHSovTzvCR@r|@aD{-HKILLaRz=t{HANY$XIWDBYNVr-8^O<Z;
zR=r!kbqBmvS0N`imR{+WvUA1TZzXRJwT>heRV6rke+}m&%71d+KB|rm=Iv|1N!Lu?
zE@|E_!+5*g&(}Xnz8=e&iNzH<HC4jsCG&M&ZsJ=(`Q?UfXN5XpOHI2q-?T$NOg?-9
z$0zd79?7mu&Ig%gDT>=M-)JpltI!SK=tB&BIeE-U7$>Wdm<>oJBfL1k-5aocZ!LlO
z%<!09c|*&Wj`Ss_%RIE8OES&h)Q5L7UpIx+hoZu7*UTk8f7%nt{Bt-ESve}Nk_$Hw
zAFSVJKHF&^R#sPVCw_fJ<<iwDo@w#Bxtr9et7>L1rx2?7VjlcoMMM&ZZTBkYw}5-z
zvY43SU?2P96AKOK61Q}6^=HY|^|;uoV!L$j4PIvnq#uH>b1UYocJ{`{iP&3jnpVZZ
zMGb%Ap2j12AqV-p2jqLUbi)dMix&E1HD8WtNWM|2-)&QLU6shk$p|rljG6PtW(&!O
zDeaw`CqDzG`PpI`4Ws`DusJ+C0RI30ABzYC000000RIL6LPG)oB?8@7-HM|y6ux$z
zrIh$@5HE@hr7+v=jHS2Y*i1K2qeORE!G~XKx>Rdq6K69Fqj!4#&-a~^pfjov#re;&
z0nOt!+Jnnu1E|}^0yIa&|8F>!Yx=wVTo*qO2|!cO{55$!*YPpQk`pGUM(3CtOMxYX
zaAf!ez3osDJUv*N4K2&l!tc>H(=?!?Yin(<E!+3<X%ohd>+hpg5N!|s;V~d-T+xJ-
zDaAz<|4JxMNYzG8(wFV3ACPN0-U5?~=A<W9P@E;S?%5dW2zxM~r!PorKFyD9rZM_G
zaK)D|i!)A9OwkET1jby61!kJCOG7lUtNfh6{;JlkvpQ=b)YHp`*>`Q9mpxMzZHsOI
z$ChXdlb;pXRaGE+Mvr;Dzo`0$gkJapnx|1=hToX@9lc=3CEd1w^Pl+j@gV!Ow9If>
zB2prC-4}52b?K#i;NQ3vau!;6UnxJrZ&fh8I6rK$>La69)~^}sZN0~O&~kn~&H8J9
zjycJxlBG1HnVg@l0?J`9D>gZZ4!9uYXFzWmO}XL8q&xUPhb;};b3Mb+LTxpT9?=OX
zS0}k1G9A%DsUA&g*Ok&OeH)0+oI&(_Urg>mTmtJ~GjS*~9*cQd;=7xKV?mBpo}>pR
z?;JaZZ|HVlc1;WDZj0{spNZ7=@*S)YKcOncmBc+kIX`b0-*6DMnZnNI;SYJvvJp=Y
h001A02m}BC000301^_}s0stET0{{R300000001cxCSd>o

literal 0
HcmV?d00001

diff --git a/test_files/test_file.bad_header.vcf.gz.tbi b/test_files/test_file.bad_header.vcf.gz.tbi
new file mode 100755
index 0000000000000000000000000000000000000000..c30fa3ec7121803aef8f7241a125e50ad38b194e
GIT binary patch
literal 227
zcmb2|=3rp}f&Xj_PR>jW#~8Q^Kc%E3CL|;<CAn$vGMx&T#oWOw*(1>-=_BFrYLA-Z
zl^YuzpDdSh%m`!)d7#Z=$iHk|54Y2Gr=y8Ao`M{)?4s=-6Q9jeoN4IA?<ZxeH}Nv3
zj@;HLMUyJ4k8Q`SePUNAx9~N09scqEkV1(?h|IC}nWy_x*w$v2m>Vko6n{2vL$-j_
z-TfZ}zAs)a>@FmoWpd)aT|oW8KZg$#M7A+%##}gh@o+1vC$F9q8-q@S2HO^(2jtPb
MA<e)H_7#W#0RGWU@c;k-

literal 0
HcmV?d00001

diff --git a/test_files/test_file.bad_sort.bed.gz b/test_files/test_file.bad_sort.bed.gz
new file mode 100755
index 0000000000000000000000000000000000000000..ca921057ad578321b3983b5f9d1edaaaecb9d6ef
GIT binary patch
literal 790
zcmV+x1L^!9iwFb&00000{{{d;LjnN#0(F(aZrd;nhR@zp6ezGuu|^arQ7jPbyz_P+
z630t|HFl7=hwbS{((aPjX%FRR>o-Y}l=ApvwSH|LzO}!)mxo>7AI~p~#kOg?L-YJr
zpX=vl^R}qB`!DN#yVz}Aeg3*xFLzsz&%15E`nf%IZ^z|fbsQf1)2jZx-2Q*GFD{Rp
z?t8s!4y)y+IoGHCx_NTJ)7jsCdaQS+?ogfk)v2$Vc2k}Af19fRb8Ph8Y1M8%#Y#e=
z1OY375g_<qwQKt3)OCkdzi+E2lfp$R4#|b}Yu7e|B4W(IP)QmAM`v}@_L@s`8iW7=
zf*`U{OyES(m0jEKw}Xl#YktLvM;iTIR1qlzWCEw;l;$ES0fdVaI^j%2feQgTl^{-O
zCPGb_I6Eb$X&r2(2r@c}lP6yF&Fgy=unObLJ4?f>?Ei1QW0keCA+j##IKZ?hXl)Ht
z5><jD-0g%05()&8VIbCKR4K}hGp&|n-H8UWDmtZU#LJRV9B8^R`gqS|1AstTEtjk|
zrF0#Fs=^{s$F3A8W<kQOKq6BnokNUnZ!4!Yu<r!ez~)4UE>B`$EJzuP0R@9R2|^)C
zM#&Bw6nG-g!7idxNJ7N{Ce<=c&H*%m6i2w*AF7ftsy{R+15AB!qR7Z%kYZGbB)1X}
z2&AfP1S5q>b*`3_(nWOLCiu96x=;3^Y7S;@tFOm1GlOXD-AuNj)ndS0v>=0-F2{@%
zV^CY%PQ7E%&FhCK;udBe0E14p=#rgagQ*Wa@OoN7ZyCf9!rV(r4B0d}ILy2-#FSGp
zV24>Hq;Ls(n`zUd!<}pc79F!-JwUyRjAoHy$ik4a5tGv$jbP4_lpvIW=FuY9ErDc|
z&}r`JeMQgtNOz|et^|6h->Hn+$qx&dhOH&hsW{Dolb$+eyQlO@g@NYVAdC_V*d>BG
zFGh1unvc#(GRh-`JDzk*wLL~<q&q4KlDMD|kkcfoe+aswCKLz&03VA81ONa400936
U0763o02=@U00000000000K*7svH$=8

literal 0
HcmV?d00001

diff --git a/test_files/test_file.bad_sort.bed.gz.tbi b/test_files/test_file.bad_sort.bed.gz.tbi
new file mode 100755
index 0000000000000000000000000000000000000000..ed075a6d2639e52f0ce237c63443b3259a5d7807
GIT binary patch
literal 1535
zcmb2|=3rp}f&Xj_PR>jW+Kg|{TYIrM3a~wR6&qXAQpMcd%M#!DGHFr9GfN*9{-h_S
zCgS>=CO)5V^x8V79#@wiRT=wc*6&)qd!6|6TwOc2*ZxPAoX?zJZFtOWzI&mJdZEPa
zzke4TeZK3u*}wB@hmSrxk#Ah@F+b_a=Rf<rmcLexe`dM5#Qgg8^0&87{xSS~t9<%%
zyXU)hUBCJC#Ou1>FOU9xvGG;NKGFNfeXp&xTlMdB&XcR|Uw@bV3Z1OtIf)|l(|GzH
z;c#Rl{)nHGMl<x}{V%fa8^w4T{xdMhqlMK6hPP)oaxyszuwDpt%sqU<L(jxC<e=W0
z18RB(Mw@uKH}qs5@Y<7{E_jxw<#7%3>Dxa~pINqT+Ttl52#2TG+e|=q0%`1%_bQcu
z4*q{boBi!vmHIc2y_Y}UV0(9K_v;gRiLyU8etDQT=X2<nr?vGbcYE!dk&^y$@44AF
z@&7UpWzGBiEV(XrZ&@CihdudDsb4tyU^O-mPiJ_0)KHK?frn*-{S`$P!xL>A*{ZH9
zMo!9Ke`H(kZ9J$}9z*u@bv){^NZEd4zreG;9-F(27~kG8^m76wTG6=l934}!GLv}@
zdJAOPABc&BUAuDZNS}2D3*SS|dCNBhPMX^(Af&<3GW~n*rk|VY)6_SM-`EuO*-;aB
z(950npQKW0wEx==;kb3*T;Bu+Z;t#?8~wQ~;=J#Z&&!@geiyWhz5d7U)$xbLU(SCv
z`Mf=dE&FTkmz`R(vxUBYzNb{vY4iNlPx*G!^Se?j%7Z`KJl|cn*ngk$^NRW(^LyVk
zC4&+~%KEwAj)WtU2G~8Dob_&KPX{yKZBPZr)f2zZ=YJNLx<FJGo#sTu;HKbnNNMYd
z<3Gly{~g(|1(_e?+gpl$%#I>#4-zj2c{Z(dRIFkS@juYydVxiVMXdFep}`Ef)&~;{
zSaz^3T9|T=TS3c9?2_4iwcYpk)u)%=>$$hdBCmQW1!))I>Pa#B@9SSW?+Dkl?k+Z1
z@!kDl=>BJK^Va4cdM#n!Wi?;^{q;Y(`)v7d14CN=%WCzB>9&0S%IB*lRi3f#trD|y
zpI2+&sy{J3_Eh!fO51Lm`|n-<A3jk$cc=XGiO+Y$e0Tja^KWYW+gQ!B+iOo$wm*Gd
zSoy<rnf7z-S=Il;`#g&}g*Q1bhs6G$@O0VVI~4a#QrXG+Y(GCl5J;YunW%Dd>K}$h
z#i={61?OsD&TtfTaA06KP`y)4N@HQ8kk*R@O(3F~t4H#Eb>Z{0@0%Z9GE=;PC28Z$
zI%U1zk+kf-b=>FtzO|j@x4-H4Uqq6)UH4z_vhza!neldY+Fz7EK4yttQSWi&5@xX_
L&A<#U@j(Oth=#zF

literal 0
HcmV?d00001

diff --git a/test_files/test_file.bed.gz b/test_files/test_file.bed.gz
new file mode 100755
index 0000000000000000000000000000000000000000..adfb79dadffcb9dfe34ccbc76cf87d7cc7a408eb
GIT binary patch
literal 1040
zcmV+r1n>JFiwFb&00000{{{d;LjnNv19g_cZX-7ghR?H4vA_bo1l@?FM2QOoJ@?$+
z3&)w-K@&T$okRQd{mGeZ;?X3B=(G8olqixj-~Qa(KaF31Km2|C@pXT>yqtgB-tNZ3
z@p=6Ix;<~dj}Nc6+uh@@_m79${Vvq!-yZJo_B*m)_PfjGuifeR`f~TYd6_<5PMhsN
zce|e-{TJ^aAC7-)_v7>C?qNJ{PmlNGO$ctz@$Hvy+x_YIJe)6^(`6VB55xKKzj3(y
z`!eFY)8_E-g@!ax!r%P=GCpCir*XJ}iE7PM2j*Bx2)0kh!(?Txm241-Wwss<m&aY0
zb0yI>6rPr)nN>1#!rEe8dY6_9Y=fA^N}UIiRM-qAp%k$6LBeE443HU8@1>MV>KaV}
zotH{nv^0kr&}G6}ZK?4fDRIEcZj&?>OX_44)J5W?R;j2{%|R;~6ICl9N^PP(8dGj1
zOLi&})O&if5a*dB%?TP0m(zzr_$i>wZ`5Y(e!PsQ<MDZOc|1(&%+;@igIZ7*JhP#G
z)JcdY>W`6yjT@;G>cy$|g#Dmaij&TiRy?6haXn6LrWI9AR%#O`%0VleLc!+TCaOVe
zqMQiEpc2&YJS#j=MAI6y<_Nom(W%XpI!~pc#Hj_fpgx+CW-ZAH<>9oV!S$k-oFoPH
znwD5m%}!J&TG@6JMQ??w&_ru0v_IwQR3&I7p5cPk_iZT!^%~2?G<ywLNkLtcrec_6
z3G*zW(}VgQ!6w4YLAeF3s94aREo+bkb@8MS0#Xp?piYCcVO$W#AkJ2TR-$F&oRlXj
zLEW_G&j&f?5(cG^uQk?12>*gG!ca6ct;^Oxvnb=BUVMtOaOj-igaxH14rqIavXHc@
z+K^d5rGV>{Kw&66G%}z~z};R9l}X;`fEuv$f@GrUk_<*OOegB56~8M07SK6kVa4zt
ztjw@FCXpjbgy}5Ri3<f~US=|z#$`LznYuHw<b=~@3MxT;#>HA9)L)PUNhit)1&U{(
zQ%e?9I+0K8Ts5c!E%V@(W>O`{g1Tap&+G6_t?~cby9|oVCUhl$Cs-y${92Pg*9Mar
zR&N4<ET>H74;811%fOq6T{%OxOmPwf@+=0GWyE)r6Hl}}SpNLX@x&BNQ>?YA&xuk#
zhRA3IGe+69<{jZ7)3w0xkkO1f6pr;ebI5`J&hUl?ka$%iUBnP>f{ET7FiHTr2$Jy%
zh4&K;s2HI`T?kOv%}|AywJl&dsa&I)$ln!thSmGQ?64~ECk}0brLS82HKLkB!Qi%-
zkyjEjO8y8|Cz>fOvh%?ND(|9?*YrOQhWa?T3jhEgiwFb&00000{{{d;LjnLB00RI3
K0000000013yZt=?

literal 0
HcmV?d00001

diff --git a/test_files/test_file.bed.gz.tbi b/test_files/test_file.bed.gz.tbi
new file mode 100755
index 0000000000000000000000000000000000000000..4a94c73b75f90d606f5edabf73177fd1f422d8fd
GIT binary patch
literal 1871
zcmb2|=3rp}f&Xj_PR>jWyBXhJTALT*D8csNX6&skOwEb5%Q#r<4+gZp;%5>P;1Cj+
z!4<<R-r$tzk<Z8~bWrxnhJ_U@%c}GnbU)WAUNQ0Amb<Gmt@zWM@AE8;pU=L#oZp;1
z{MJQ@Gj?lv)30Zg-OZ?7b7tM`w|={CzuQ{4X>ld{;eWLzukzwv|D1m2W`FeIdEvDZ
z+b4(bwR&Oa756pj>CJNGuYP~#?YZ|jd5+5ZUxoRbVr9S7<gdKG|MBKC>r2%?R(<;V
zCA!w$KkoCg!u*}jx8BeDGxO*EAp4X1^e^Rqjr{xf#Gk5t^KSpTP`}vf`S#OyXTSZw
zaqq0+Gk>E$UJW{b{N>_bRdfHY>fdD_`?7Lw@Y-_w=Mk^3RoD3bzX~*I+MZWd|IPXT
zeKpem?*H<kWc2^kNjC4KEZxmLCaHK%QmI_`?##{a(~q22@ziS&1`7d2PYTb0F@Zdy
zQHl&dlG-PWcGWrVdvgEdI~MziD*8*=!3OEgsAu3%*tL)0KLdk2THH-ye0%Y%mTMp|
z?%vACq`yedNk~#i&C+6anHX)blt*F*gZKiK=?5Do_QW(!F<Rsk!^Bp0ZTlzV2}0lO
zo=0x2j>^CP>)Ls}Q-xPGxS-Cyy6NU0`QzHJF4^z?d0Z~!%4Yeh@7~+0{$K0N-{n*H
zFwEEH&$4ut`m?uZ-FUTn*<{herQUaykUW9U^VT;G^L?Cyq+*lzUUjJ6Ylq70;l}K~
zd9rKwuagHq&CV2e^?!NC;ncOmY4NA}qcZCx&*?4uqxMSb?Gsn!r`Iq3)|?~n_0#Xn
z_rvWg&X+E}Sf9B5&Chjq-{rOJ`aVgle_gzPa)IV2oAb|ac2qz6{kApOR@1(>a^LmB
zFO_}8y{>jLm3H}c^CzD8Z2h$K_Qw2s`tLvAnEh$%irc*Be+SR|e)|8@%3p7NJtnPb
z{++^J<pd2R(+{k53emdQqGUb8+oKx=9UKH04s^e8((MZDu2Yek_@cEzZpQze|L>+e
z-pVg1X_tF@+uxU`w*e{Q(cLeXGpt{4uCLYn^J?9_n5T!4^=j_JW6)c-ItHgJXYXQj
z?`MX$XE$;(ISQ~|_{#KN=g<*0JrQH)t?b?#cnuA98LeaN-pH@aEM6vl(IG(KNHzE2
z<bMX6758P!9@0+dg-00aj6bH~z=ZIm;qJ%vZ#_Ppo_Fud9NFWml6sSJ)irOY^IOJ0
z*>~o8=&99rrvF^#z1^$s<h6$%Wv6HE|8qJ0w%XIbm;deAdmnF}`*T7%r1zT!Ha|}V
z#*rZ-g8~ophJ76l97!MYldYd8o}9d;S_m^j-v7Rd9MB-P?LTx8Jb{lU^;V?#=WKRt
zt}<nOd)d&7*-?b;!NnUdk`^va%1)nrO?b`Rh-&8DCi5KDxE68vPl%3K{+%O9+{Ebp
z#1@B3tvbJX&(xhcKl}LXq|-IFa?@cc6q3nO?$;=KPO|=-+&w?h_&)o_bam70*{`mr
zo>iadfB5?1S?PC!Z_K;?N4;vk>)+Tf=RX^K-X6p^{gwAmxj*&(r(f;r|6Q3cV&^`u
z`01bR%|O)_dv>j;ocB3)|3&rt6N~rU*GW^}o$xOiWZB6&t2dqeNO>ESRZ`kzHiq|s
z6UUtgEf7iRx$kxwL-SE~oH;_rNxhp;VT2eYUELJ?&yc>tIR;y(6$9gPp&&3WSvGw4
uIi{y`_?W_h@2i9-#}uoOA4##5ruW~!XE46Eb;_E#n8mI%12eb=1rY!@9E98e

literal 0
HcmV?d00001

diff --git a/test_files/test_file.gtf.gz b/test_files/test_file.gtf.gz
new file mode 100755
index 0000000000000000000000000000000000000000..aea9ae66976f46c1d5de1493f1bacaabe215ca76
GIT binary patch
literal 2522
zcmV<02_^O)iwFb&00000{{{d;LjnN33GJP2Z`(Ey$6q_2!b@Kc2}m9v*H>A(b_2Fx
zXg6Tn8^f`+)Iehgwli$sen&}u6eU^GMUt}>sO;Dd&HL$p$2*cz-hA~C%@>c+)&2AA
z%XIkR<LzfK*H0WS-fZ6aD_X8*i+TFq?)B+-9SsFz?uv=st8qJ5<H;mi#lLlT`|S_k
ze7L<CG5?QCrmne6J{~2X{W4yyub!WLb5m@O!xeKEZzi9Yi^sug@w}WwgFmD3`gs`*
zR_pO{J&5Mh!D_OIe_oF9hd-C&$7nEKua~p?=XG?!2T#j|??5yi`A@7S%h?nD-rtM)
zfOD(efD0ka;Ck>i{`Wl@&8EZ4@9sW*h<hmnI3q6K4tKx2`M@vn2c*&<EPlW@IhsE|
z-bc&fCC3-y#^%_a;pMw`zj6NK_Qk}M;bk;mMUVGiMxV!jjpyUdyZ5uj`kyC!`)L(D
zPZ$2R!|y+6^9uWT`1YptZL4w5(oTPu8YP{Smv8g%>^)5(Ny!`mq`olmhHqPnE!r8%
zMY*A*c3@{VUA@Qi@I2q0lf6!EBx^)d$ttdd6dg(yJv)4Q($@1diy}Ie)}ewuv(rv&
zDYM=ns;C;-Ts2lJ)v0Pk4b^D0O4d}3Y#R5r%zA^UifT}U%pX;w;gJFBQZ+2kk@AN}
z?xa<c*AY#E476bc$ofL4l4iIeNU1`aX)*ZL(Tp}+gRKZlIfX|fI6;W%3Rb<aY#4UC
zA}!6qA04^0pgmf3q-B&925P}-D6LSQ*s8Ru=ZT=16=3pf8#+GW(yv86HA+A5T5?sz
z<P63sbR0qLd9qDdH9XHb2Nhv~KuvJ~%pQqh^(iL^!NU4X>N3Ym@DNQWbQi^|&$$4`
z98i_Dq{u4Qu3*)w_JL`3dJ3M>k_>$EtrT@S)hewz=@h1)uBx`A0<u!&fR=8LR-HIy
zH87_u!qU2N)Cx<h#SyTUw15FvKkX)bR9{E4`Dn73&gKvMbuU=U<pATq^{#gn<io8r
zzzg_*Fj~7q9Pe*_;+)-9#c|Nl5R$areEnp;VLg5rUf$lm`-IOYlj$n%yZ>1VEmeq5
zET0V-8@pKv8FIsuPUQ^6II0MSM;+JdHBXwvFs)@t4oqWA(OHDbQNStXxXMSg_cR41
zT%7+l1=S}mrTXB_^}(6Yo$EtX*9Qpa@tvp-eyWd`g6b2OY*1UR7f=3qtPd=;{gEeT
zvqnL`TYbFTD1h(9jP^ZA{7>rbaPy_9kw2$KT9BqJFbRu!7*#wz!1*GhFzvu)u_!by
zB((&N!Yq|673&rbnbxutg%e6auEQQdBn)lm3-JVpJsc@;gU)8CK$7r3&%jWT7vi*K
zhAgG%7FhM%%POaBf@nNn&sM%OX(5g?(SDZ>&dai*nR~-@AsH~nm2KL(xn;)T=dR5$
zoE#|IzJ_@0TB|p?YH%H1A0gROO$r7}e9aUAm|k!=F!mwdq*cvKA}g{w6n@25(%~-3
z>AK?|(4oQw5vNO{7j6PD!0^FxtPt|z7p_HdUx62;XwH<)EqwYOey=`XRvNyNX0MX?
zSuuLyG_*afa@>KkS`&ck50{+ju#Lf5gF8VP)b?b1_3JMmW1WJI&jM!+&H@9&+f`@D
zgzgE+h>`#zx0u+HaV#Ego02(jWOtsZ0&D70;Uq6BnIqq@)JQ`RuslO_1@32?yB}AK
z={CWfu&|j+L<=iR{LVJ_yA6^9zcXjXC{(>0Bje3>r4EM>{dCcPQ&+j^8HOv@TwPes
z>&$v4XKkWl%!E<p=Vt((kv=g$OGs%6P7sjl50?uFhGOu$!~6qo=E*H<aO(i>^DVGf
zD6QDh@P7OK3s~zLrI?bzxj-FalDG>ol%hF@GoTb)D{~+r1aRM%5{y!D<`@CS^P-kT
z^AOiV)u7PYjD0$u*1+yyKk%Vw`9KH>+!n<<B^)nXs*3sEd=ke-<aa(3s&h{pHd}8K
zzmU?hn9MR-k7slIy4ifaL^MZyloU<);4023q2Oit)R>rM5;yK|)SQ=IfW`Hb#_>{G
zj=S1AjF+l19^3+(EQaI_t`uBwmzi`eVklEde$j{ZoG2PqNojPYlBRe{WmKG?rWCDJ
z;0S!JC1@qCRhCD1lQB>$Pz1th$z*yr+Qbx`Ic^+lacR}s_F(8!V0Z|4e}~cC`^_tl
zAMb9qFBQZUN+MmwmFnvb#%U>3ZF)y8h756UxRHi{VNZ~q$R(Q-W5wYgtZkC>VZbuo
z=X}-o8)?6dz!s8mOi1c#p>;CVs|CM-SU^!Eat2~NiZ}5h&Rv(0$W)I+;ICP#9f{I`
zjTBx_SW$##&jqw|Qv4UW<QAQ{VcQS;xVJ$yNrascvO{N+m7UFEqGRQW)j|RZ<F#c3
zkov&{4WBRO@wha4jHWYx^RUr0nvDNRBMBO9l7}WGk^&}KdqzWTqj&ybn)}1X>aP5u
zdcI<WvziqWI(7-%X(^cnPQa-jSPE?4-<Io*2bMe}g9&?$BDs*E3_}5qfOrI3Fpi@4
zup-lODFSoALred-d#{`#w>4?@gm5T>+33z(MPP2xneN#BY)B9c_l?JwOvr-FDgmTz
zveNsS^^mAv;AWeq>c@p~18rJ+!fo;L<iD|35!l<E{OjF1(ODCxh{gK%gftUQ6A<bV
z5VShDn1==nXe<fjWqGHPsIyY#Z~rP~kj<eakPu!d#|#0X{s77P!G2cc6|t`i_G&{#
z8ywCcW5{Cg*8tL(e-1JTU)hJ(rr@aYvUJWs9C>hX`Ed&;XHH6CX^D(5)Vc=Y6YnXS
z-DTNwidlK52=1{oJiZ9##Q_0UuiADDh&Ke3ajzpXgznWc83Olu892en+$tRU$V}%|
z=Yc2SR=6e^UuyD_Y|g>23ekk?AsRNJdZ=YKiZB|dXdJFWYQK}8S~jf~%XMUft36;u
zek?vDBVH|;CV3!%dctW=%Z#e0Im$4jWVvH0Mm<)wil*j0PH`C?N<Aw@BVI3>vMeWO
zxJvlYOip#jr^axFx1De-zClV*IXH(aZ9J0;F&R#$9N8ur0_B8a&JGX7M0c<8WR-(=
zyk|~?r~bBg_VaAy9wEX4t7n7|!{ZD$8KuflxP1VR_=h=il_8kX5(@0by|a#ILdx-^
zmcxNjUh^EwGbYEK3|g8tR7(xG4B#BMdl>do7g`t{+rBl>H(kxN<~`4e(s(Bn;g6b8
zXU?rU8A;}x4bll6qSg35(+Q34_{W4;S&T;E@c0PSGlcyD6yCq!4VPs4=#jPm0(!2P
kF@|*j03VA81ONa4009360763o02=@U00000000000Ea5j8UO$Q

literal 0
HcmV?d00001

diff --git a/test_files/test_file.gtf.gz.tbi b/test_files/test_file.gtf.gz.tbi
new file mode 100755
index 0000000000000000000000000000000000000000..a37e829968bba91a2fd5e7f8fb72333c971cede3
GIT binary patch
literal 220
zcmb2|=3rp}f&Xj_PR>jW`x&?kKc%E3HZZs;ux*TNjF8ki#(1QS$BpM0j~b7U!?xuD
zE_Xv$?AgQ8@@>`;hH38N;;9a-C#q&TK65;(w%YN?y_t(<u^Y3i={2X#GrwYMP-;-j
zGVw@;>)|(-E;n7Mv$~O)Qg0RQaOB(%=ZqQliT`$sGAvY;3~;o#GXKS^lnF;(_#Xb_
zlr1&q-3*0)?LTKXCd#Wb2mM&sefW|-&jzKH2VL#?oUSr6^ha)wmSJXKkVkXBGy_l&
F3IJwIQJ??-

literal 0
HcmV?d00001

diff --git a/test_files/test_file.vcf.gz b/test_files/test_file.vcf.gz
new file mode 100755
index 0000000000000000000000000000000000000000..b0ec61c147d8e16ae0f769d258a982b20cd1e93f
GIT binary patch
literal 7960
zcmV+zALrm7iwFb&00000{{{d;LjnM29Nb)6bJ|E2erA4!YVtCvB3PH!&0e;O!GNg{
zn;7EkK2ZW1(2g#wB$9Z`KYmZEB|xHe#W>l`)Fh5{`dq(rX{nWW?^dRTSFUFpLHnuO
z|At!PZ|~mqhofolvHiE<ZF}6AOq#dYUwGy=FkPqpd&jakSQTK;=eCCL<K^#vhc$%J
ztr6h1$P0)Uc^$6#?#^4_Hg<e$&#jwpu!OKs(ap}Y+M6KQUSC~d6}2LYmg}vrHm>c?
zd}C|EMd0D#751<LY*ryT{GK4+?&en>wy@#j4=TD^8Gc|Scw8+V;|drJ@B0s-Nz+NE
zdB3yg*lP>T>GKx1CxK@=>!g|F2IsCgAOCwt#B&BQ*&sJtTz6wyOL7-3*?W@NfrK-B
zZi!c>gO}X=nF}`fz{qt1*K*g-+}3mdg%?39^xs~+r(UdGD_gtXY6UBSuMuztOGj=4
z8W24WH&@sQb{?jSTnL6`Y<<oQT3nw3VA7es3~&GO(x1Nchqp<s;9d!*O&E$07o|)D
zAt`1<C%|j$CAsk*<`C5-XF5y#gZpM!yGVI+iJib)nb_yPZ_LF8?s=x+1P5D*!!h-d
z>2q@onnFAX?>R68z^63om$9xNJCHzwDiZTHLRom(;-(w87{bEd`2pMxb(uV*pb`he
z^&m<i(9FQ+76ey-_Oy1x+Y*@Qy0%Tiy*0q|#L7s-@Ybi=E?m#U{?>JtT;RfG&Io|b
zd>4QpO#+oczb}#8j;xCvmV|G_*602JH*)xgVQ*o<8ar?aF4&Lv9shmGfQh*Zeio_;
zqKW+3=P~{B{)qu^N>Bm>pLd332B6J13<->v<|0(=4{U;$JaDXqsr$hfOQ=hry6Nti
z9sx~C2m}gXu`sMC11RDN$RH{XvC%UB1M;An%#FDT$~{wOko$&hIxc4{%q3vUaMn0n
z80*;Ne3$b977#iI8y@J-bMOae!zIo#|H9TYfeJw2$dr^NW7m4#Zm{z+;~VQhV!Z#E
z73U+uGh!WOEcH0JXldBSnyluwuJ4=4OLOd)YlpyL=ltck-<|gv4txbToL~SPxtsfe
z8SFyMf$X3d#6D!PkG*h+{laxtVU@L>W6SZf5DLrr<bFI8BrUdsr*`x$BW1-CE!a>*
zOlM*3mZXNlTAwo<TJJ6YJ!jfm*9$9|=h|GzoF%VonGW!q!QdeYqQsXM4l!K7;?SEu
z1PNNo!XThyNWO~1BsJ(hOg;^}Ges>FI&lH4<^sAx5JKIDF0>1c<u*IpaJW!1%v7OB
z5=_cFo)S`+0lakGB`y>j6Ozyy5LU}F=B^h*I^;~l8bC+^p-WI9AVDA+z+6Rj-I!ZK
z@*QJ`RC+h;fP{+Rmi{fa!%r&On~Z0Q%ohh`3i8%21cFRe@bmrM=+7ZHc;I?JTpJoF
ztp@}r<4EnWl5tBD3K*0HD23m!74;#anvF@tGkx19Xr_&hEQd84z<bc-tR3mxKsvWv
zcS$(89<iTHZ2m!Blvn{Ydf*g7)x+yBgpsZ^fW$GNsj={&2mm)S?&2l~$-1$gKkPjP
zPII@r$gxRh-3>n7ei(oGa|DngXqL)DIYiCTddTwthNl1=w+%31!V!*1c@Lx8*{3g~
z>98{z^<Ytn^7G)CP(2__i;Z^;)$SVR^J^&J95^fV&8dW^&f~CiKP}N8$}uO=G}j?}
zp=n`f9c<bn(nXn9L?J~W9tb2s*Cka-5lAtCpliGcRD6m69S8(LMxv?!LHF+Q;ZtM$
zFlh{L8;`wyqcfT|K7Z+q8g%Q_AP)FVXehdb<OWG(SgZ?Lqub~-TJYb#Zrs3bq&>NR
zx_Rog{b$E@o^7bBvuL1w;a|u+_0qeaOnLH4l4L<rZy@YrylwL@!;@Q&ctvgvL+P?8
zg`$wCC<rwMjcK-Y+l0LwY^+Ml?w;HtLk-+GY7oFAO%%5~AdDO6EN)6KLY6%PYLBFa
z%B!-9L@=lGispREGG{+7z3?qX&$TD&{s(*bmL_MJ^c0z-hXx1|k`$eX2z6i4s7@K9
zc)6-kiYygag?MU}tne~Y@{v~q_fG}lmB^{GuIsY=%1#{@J5|W@D4hrysS(*Q0vj|%
zkaX%pr0@bSfeX85xlq<MO;nq^tsi*UuxF%G9uWr~^zN_}AC@S*F7j%#Oni{YD@qwk
zAQW`I6s4r<id0Eq2?@L+A0jn9F+UkSs&(R8q+jw{s7V~2aTp!|HpQ4EDFT8rn}_h~
zHoUUasVmEer!Xg|JJ~tG@+wt;?diu8wz)lmZ|T~}ila6`Vk4rc>xwF=L}&HA2sz~g
za+zpXjbVNkOc?Q+Fyb{iVO!K1bRjD^lPEYcZQ_!G1VuY@D2Ws;uHn?kVty2qmkD8v
zq^)JbBS5-|I3nJ9rfqo7GnSBazI|oH>MJ9rUr$U+<Y2^>F%$@hAt5m}C=7844niJw
z;wISQRgEEueS0q_V>OkMs?)kaX8}c1G+8;b7?iD#W${*{D@S-MnHmSkOc+pLm4RM<
zxro>@Aafdu6e3i$05Zn}ksKyuc%31MeS0s5*+^7|tr=oYX8=_YWxBgV0#ap^zagm-
zVx(%Ss8>P-l4V`3wj{E+1eQwzu3By^;aO+}`%-BBc%on8+8z}j({h=+)D|x>_@zih
z2Ky9=a3ZasU8;yBcn?8I&P96Sb|f%DXfH%4LP(|6Pt|x$d_{yRO4YiBKpRD<74|xr
z@UviD&5KA!TC;j-IOM?{13q^Q%-m(=!EybS5rbP60kg!*a$W`;l~yqi_P{*9z@seK
zKSr=8jXs8b!QT1Ou%|J8MVN)&`i0V{I_zmBI0yCxJN7-K#${kH6%8(uT#y%%QU>-6
zDXgA=bS)=2ijc3+t*;=6Jkp`ucUaIjA)+36=uQ$~<ry}HcRcV$x&WNf%h(yVTxT7=
z!2rtinTFF<#rz`>Rpeg_df{Ys`Rt)tU&{0_z?Dr8S6z5Qtli}kTYk8rtMT&~4F-}k
zAKcd;A208(a<#rr^y=2kIsq@)tTLwYXv0-%LT64PB7<ACF{R|AhtoNtdDf7U8op&-
zIKW<ey+_2g$HvPbvl3=5Gf>n>)%v@U1MEi(e2h*kPSIs<LK)05?z6X_Cqh`57c?~w
z)bKKcA%=ZBIe$!I%t!NwBI`&d??nb@)%tRKw70@cje=Tf`hSz=d?x508TffT2}R;s
zvewrG{ho1dQWU;B(shPNHYKY&6jCxCLaRts={pa2%MXYk8`8mRjOA}PHd7c^1WpZ1
z*BQ?xQRNY;s+_9oYUL?XlT<kCS8Mbvv&*6-sp>B44d?nxZ)o;MAa0IMj<tnrl0q7P
z-M#8|SqTLXHoM(v7k+i%hfa4em<~FFL5Ey`|EGgNw*yx~3ZR1@I?T2dR+cFJE}tGX
zwj^(t9yE8~B0Xp#UV1M?5g)yJUAk~^{%A$so7V`=^Z?>)58wjyn{eW^^vm5;#suEZ
zS(JVRU^-z=&SLClHHktxT1O6je!%E{gA?-j;KgV>xf}Fu$K$Ve@Y~%TO;b%kM`?=4
z<EUv-->Z=jmu{7{(%>8jT<|GS={kN^H+qX|L+fX)VpyYeT)wJ>O=Lefo_0V@kgum#
z)9G(w1IZ9anpucfbzaRsSzJvGqDhG@7aWCF^ro{o!t)Wavq*wT5qMFlmJ@W%p&;F-
zg_n4hOX-UC1d@2NBnrdF(AlymM(0T-QIy2|Cpl#fic#Oy2+JF~yO-sY9`y-|&eiZD
zylW8i0r<<HsfN$lr|t6qC{zYu;*@y8*%Rt)O+U(Z?aV_={}b@L&2o0)j9H$i4^L_Z
zJ<Gj=(7lR6-%mi*M&yHyJnvrI1<lJ<>%8P<cvsX*xmV)leD|tS{7ewe;Hl)L<lubt
z{)%y6KN-$071ip5kmcn*^|Bg$>;rHYbb#>x{Xo!tODBhg7(T_IP*z1jRrvg;+ZXr5
zn^cOjQ&)b|V;y}HGJXA#`Wn$gJd!NJ3$&kIl`q#-nMZW9tFkQSdHV38N7S<1JD~1W
zqnQFeG=*<{UZ*Pm+B3ynDJ)kj80l9E2~Yo%dODuoBp$Ys%4@y|4n0_Y$MJ@~o@Dui
z6jD*pwCFPs7-<oF9h-kB#1Gu<Y;BN#Pv`VG1uwxTCFM<%;G=*hIBXU@(!)OzHnQpS
z6p&;^kojhzj%q%MEWnZM@@DY5`rq=dt+#I62tRLsO3((nUmgP|UK@6eIP2QjryxMR
z?E-Crdb9t(lt}7`;z!PqBF{PAeU*3_QZw_-42Pp8WEpe&yT8B3!*6I2!HatQYyElp
z;Lo4`@$iXi>R)^-?p6Dnhz%?{Y70feJ$rxpx-3HWN45_Q@`$(<pQLW6t1{%1P3;c?
z^~Pd(<C)?@yIsF|Ci!gBZvH~%Gx<rj<B4x@$T$RoT=)e!FMH?J0ojD-40)QNsrKqS
zS}SlAD@$=q!je$8Bot&Qj6i6CfI@-CLTf1tEXeAnTvZA0W^d+>q9m_G(o`Jb!!kSr
z`K8WK%sCr4F;AdTI_YA1XvzBw5@z1drhR#P&_gd`k+&<0=S*)y%j%W2wdOOe53a2B
z+kJc56JO|a<xFW>T@H|@+cSk;hNp>Mm6Hm!LSh!W*vk4s=dyMfd|2PuSatyya2ddU
z;Fb;87J7EQJLK%kKJjK>F5bVN_4`<;bmU6x%vk#mY@)PDHW7`vG0&E6WzED)!Pa0i
ze??6pyK><+Y6{tv3k8v@n7VRRecTjt*Sts{MVOi@EBMC=h@2{`g%-DCbJrX;hxRBU
zs8U^-)<V3P;OcG*NL(AuC2Xy#VJ)C{ZAqWmPD9C~wL-fuE)X&R>Rbgvu$^IEsfVV@
z+X7*#JK@7+O4MMP#6&$lOKy;1<G2*0SABRrAOmG}P|dX<8ly0P&n_@pE^GHp*&Bh{
zN<_Cib>t-ixkXyDp)JBQtA=69;NrqnHk*X2Yq-#z+Lw(3lGI)sn_3x3<x@Mi59Ay{
zQ8|RO+mz3k7bQbUDn-T`8;R(4by;@7*_UHqw82-2`f|#X&uXOMf=61Hu1}@3E?l?M
zD%tESwfIk#6l~flE&P-92{r|krtOCLHh^HGJW>g$cO4BcOL5O2m*uKs071Pk!Ge8j
z=(knDYHKI()!ZIz#_BcNiWR7#jac=r!9F<V1`v<-z(cuNRH~`04N!Rd&cxfYY{sG<
zk^*iRb{<0`@O4?AGr|ysB&h?xaZc%ZLDRr08l$8t%3S2)Svq_SJIaVNyw1u{k}%D*
z@z{WifE0o-0$2G>X>f%AK9d;%xD;HHfK1}44TphvN<zMk*l~bMK&Bs$2}HFqF$7U5
zu(vm04Y(rrt=0()gQ(L{>^=CD^q-YHOJq*wiK-8L6z^*`53<32UhK?^7+idd0@=JK
zOTs7v^LQl6pk-UjvkwquDa8Qu0dVhu+FU==%5e2;QO@@kqnOXMmcF-k+wMDTpSb|H
zX#m9roT2!rs{!_b8?Z3v6bO@B6vFjRG5DtNU~cKfJ@GRuuo;f(RW{~!1K5aFZ)BP{
zUfXzY4L&$YGcosriMdTvH4Tw#lui2|BU;V$6ytQYR8V<!btcy#$^i_E#m1RdsUzFR
zal4sOlw)|ZY5nsdmpRI{iDjlFgj_aksu&>w%@D!?ygDF!B9o};9EpcLSW6IS)36_c
zs2tdzHUmQLPE>5bR<Hrv5BDLMid<|9uuaG<1-a_Ne%ZGJamzWArOee+Q72MS_$<}H
zSt)aAGMrjTbAzMOlnS%a*lUx=h5WUJ#4XdsL)czu*cGoh`{k^xLGE!t5Yof4!%DT7
z&$N!cvH042Cb@FcPHFcWiyyY*N#E$k`p)*e!=@~<Tn-VK)(bP<Q-Io(V97>g8Z6%!
zpaXm13~eLOuS>8?>jop(G4C1%4~=RsVSS4APbrq|WW#bff~{QP?f`aj^|}T7xEg!_
zyXdkv?5KMKw$MZQ;3Q3L-}*w(%3^3mL5ZqNYB6xn^0+EE(w|IgwnPO2xe<aGpyfhW
zUSs3ra37Qhl^Cru+m?BaiLCLNqgWubeUB{$gysmjk!69b187A6>i}6GE=z@NF_3Uf
zp)F-{&;|k6iXeM{v{}Nfo=A%!2$n6}rR)vDB%llmzezw?E1|Xy-(skLn0|!Zsggb7
zx7)-&k-0$D)`AjVR9`lw^|vTkIELP773Fj|aN3O3$hn6iZmW!p=wl`RmRoS<6<?#M
zIZN-mVZa$Xa#ze}aye$kjwIc9rpVl6?93!>=9s4^O3f{lxU`F=$|d>>iH81b0lmfy
z6(HVd&{!*>Gimf%9Iy3K@attED+%quG8}{JMYu?tm$3Y(Knbv{gjm%=YgH*L6)^=!
z?pJC7I-#;*YJ^w`z6HE?3pnT&u+1%C#9P2Wx7PGPf`<}N;u1h8p$#RW1EmCp4p8qh
zf}9fUkzTK8t`p5H(e%i?M`B57m8a-^T~s2X|KrZG#BvT+IWf6<&X{twjFxK4Saik$
zIO{+A^Eb$)F&w|JoHyS5U8QEQkAQVP0#5q~`1a#=T^j~!i&mWpHT6(TMMEzV)NY!$
zI>4_Bf`(il=2XU5I;@l2!G;D115TAs!-|?79YNQCl0yTeHrL%dWYer0lz><lEI{Nj
z+#b0M@~_2&Wru7tWMH}mSIfY!5%^Tr5|-+~O4N0hv#{*iofX70E6H?b6<c=XhM$Lu
zV``#<q+bHYy0kXSc($<6CE&VCz~-0M^p>QTfDHWBHs1X1n_t5HmZzm&9I}n5cf1B(
z8=~LQ8^|_VfzPm9{*$F-yBZHLPL*IxhjU@B&3VYy=~PyjDmn=FgY{*MXA3hv0RDXd
zeDwf0^}(7Rmlmr4Eo&exMnIUST8F07Qx-&%?QQ}g9Yi{);$amEt)P}&--2b*E%j>Y
zmU_`-%Vq71G1m^{JEb`4LMje%+EcXs*+y)+7Pb5qC)YGQyFO2>>!3Iu0qZ>i#(lI%
z-#k;y_z2kU(VCw8ClfT`q2e$abb!h<YJ<{oIH|<==c{Een6E8+!F+8Q1e@1egTQ$0
z)d1}{SgYA+fTmfQ4y8W=aB`4+Et1XDSE(&6$qSAU69@@`u+zfIREP<LqSW;0cn9&b
z(Ey3J^Yj>Lko5@?v`vgDkcu&Wm?4)E8y&Vp+M_D~*+D^LMe0(tYZB|e(_-C?qMS3~
z?t5!+t4ME5#XQy3S9n`)MpUsp)zvq;{6JBoXI5l!<wj*!?}}vvKWfFYt7mi_p^q3{
zb<L~4<BCnnuD(rGM;I}qZ$h$fEa@=IvTNP&#^S`yGo@bMSUYUCGXjD4N;R}=)zIyY
z1Tu}-z+iV?Mo9*^fky(l)CoK09~R5!o)-{*QNp%3Aj(yQ92)9?SjYQ?a94l12<k6S
zFhzyYQZ0^bc`)S3F?}J2VSP$|2xE|Ag5yD<DpV=5N|Z(sKgN8Q;?N+O@NrcNS4jB*
zy7}YhRZ;m>1(mA>a=#X4CUU<}j+opv#xDzCOpq__ls3WI;4KW`dlecPPi#>(3f<Bx
z+%58x;4cPxlubj9>5V3AW}i1fDU1iDFgh7eY=)_U{~x5UQ+`saFQ(;`IGrF&9l{@h
zE<Ac?EysMOx&97t?H%CHJ8OEvv>=rMVR}%?CQ6xDi=Z?GOl+fD`c4VVmR{{+j_J`U
zLkUd_YD_agajiAQ@=wfB(6`sLIFIA|#0C!AyT}}@2v!w@#{sj9xE=@aYCNjqEj)P-
zwLae3*)`r#NRNYiIuZ2iS--0>j$oB^%S9VeE&Z;>$abDa%O%>zFM5@;*i=>1RYG$l
zII(yoM~h)cfhW`mVMYr~c0dUWDA@reF~CF#m=w`F(%D-ooxSttGnoexWY!@*v7izk
zJ1b?7k=x|YFWQ&egt8t3@~Vs!g&QUA)33@Fai1=gT_C68SHWd3-$i70lKNj>zWn$3
zw||STN-^j!&tJa({__0!`9I&j{_D%sU$p$~`G3DZe-*J__15l1kFRzjaD3g19$$Tk
z!10d~T@Bq+)r;}XB<qHbuX-`Ym%JZ3zUsxHe+KAa`sZHRba^N_GK{2z^lw^76((18
zU-hHk@lWQ-1|G9#+reb89T+;uD#rLXWZJ~Mw!VV#Y{7wRYZJ`A8f~t(iwm&kgCMg(
zIr^?!o~{%j3i?Yc6NxtDVPKDJ={MvXuvT(R|2f16LzVQ3*1<w~Bcbng4Onr3zVZL&
zgsTd&N<>0AXF45$`9Y^sa9cC}9<b;=V6l5^PmE^^)7}H7ySJt%VueJkj~Dgdam>g%
zxF8ipkL+o(rC+Ff<R8G6Ey@6=$Mh<S-su9!W5{u6m37hgV^{A@SjZE6<LZVJ%BW<P
z!1_5y2(03`;qG{#FH^w)YgCWHl{kn^20)JEej*G66!tkhcH_}80lor=9C1V@evQ0*
z>o~#8I2?z*TlwjG@m$d##jGb3vBXDzM{(DgisK-qSAfl~0B2qSe!Bupc4bY4q!diL
zvC2`#y{8G1R9Jk)pN5P@wf0{H?$CLH<FzfSo&PFuXWcX2;;H__;B@O}I<Ze!*YVUM
z7-%w|g{z&=vDk>}6X3!pz<N)B-<|-IJy}zc*M0Vz#rUj@bklu;3hmI6eVWxG@ugd`
zEo;BE-a6&`la_B;#A&+IGq!uL1HU$B^~9pO$IK2sXiw!oJAHHn#YTZbgrW@+q|gu=
zx;Sf0V%>s;NL>1%v`3l>ceY@<tN@Adt$B|9=`YO>Z7r&|s@hFWRZz8?<kf?Je*60E
zWyKr5n+L4`cYb+T)jDRLVie^E;(Au&z&37G>zH|}PShceqp+{LfluMwI;1L9I|`|f
z+V)!1=i`&6S_hFPOxV7eI8~I3k#X8uR61=s|G&Dz2x2Q=)t*tlOMh)fOUb!m{Kuv^
zkh_(%vPTb-ZpoRye*ON!zPTj(z|f4^V)NO&nTN6@l5b>+Up+KULs%havQJUpm_%*0
zVcEYHgOVVgkCRe(aJcZywZ$|3sQuE>^<EBw<7FKf=kU68vG1c~UsW4J+<obae&@yb
zqp`qQ2vVeaKed=jCRo__9pIjKM`YjieRROSbxrVZ+aLJ1OL7+@^1CLNj-22BJR~Ru
zWd97<=jZJFi*o_Mh`8b4V(LrD)P13BioOv_*=tjr)LP80z_Z$;nH6}H=o}dP1K_3)
zF24Do_(s~ImH3~6xXAjDz=t`@FYqT(a$HD(k#MyI<}=xxta`WfbqBoFP$4%rmQm@J
za&X1l7m~M!T1S$KsuG;NzlQTU%71d+K35$b%-dIhldhP&UDCW=hVgc}pReCbz8=e&
ziN!B;YN~|MYv${`+{Cwn^2-g|&I)zHmYQ~JzG;Vkn0)vIj!)#5Jtw;|IUi(}r6_L4
ze519HtwJ|^qc1V^<>WCZVVtZ+Vm2U^jPU9JcW=P*#@Yh&nc*?J@`je4j`Ss_%RIDT
zNHWde)Q9&oUpIx+hoZu7*UTk8f7}zv{9`x}Sve}Nk_$HwAFa=4KHF&^R@PAPB!2yi
z%4MiSJk#QL^E9bZzp9zNoI<GPlX>ue77<Atw%x0oF97#ku$b7%!T$%vqK54N{{R3V
ziwFb&00000{{{d;LjnMk0^OM3kD@RT$Di51#hCJ|&=?<#*%*`6a~ETBPlVO3*F*~`
z+~r94;}0lC5O52EA*U|}r_-VH`OdUu#Qp6@AbMR}TabKo1!{&m*|?|B`-SNgL>_ZL
zozGKfADpvuB=i`8F*3B=5P)P|8P!?pCFdXbYlFS%&lgS7k)|SP{=-`7reP{bT1Z=I
z9DkEX%ef7W$<~@pt@UoQd!70rb!m8xL$?1oj5suiLqC74XSY*~=-v*PL;XD?UXU}U
z`=T{akSUL1ulC+O#1Y&0Z~XgPdqMBA0-)Z&duA`@T~(0^O>yrRd(o9K5^F*OR&eSu
za&}ml^HCZjlBE=x$<AR32q1bZC9wF6n`hj-ac(p{g+w)FT~(y{qug+a`(K@bWOsnv
z3#<Feja5;Ftde=gjg@f&Q%Gc80}v+Q%<94EABQvXeN27a8JK-0wk4F`zhkqa-3qTO
zG^+||RwZaG@)g9!2YkW-W~DZH8CdtfKpT}sTPQ+xNMA~!$xETCASmB&q5TuxFR8wF
zB71Bzd?XD5djjNb0=o<q-qy5w`zMI2U0~v6pUb0N?mO6Npj^l3Mqkf|Y_PHv?SSpG
zFWi9sM|t&L@UPmMS2VQw?Me-%vC1W<nd%o@^}3u>J%}~GxO2eZ`8l}MWxX_|qRg7j
z^Q41Ko7kEmTF^qHc?$AwGO}6m<kl%Z2<EOe;QdoZ*Jl8}PR(-2$8^0@AL=f$*Dif6
zi0>7J=>2vvD+}TnR9&#$F)5ct*Z0ZINdju9!fTbK32M(A8_qW}QkV@@1F{j*{rH}!
z-&{VRiq5Z(+V1|kzy5r@=`SmYTGp|%eEA0fU<H_Q761SriwFb&00000{{{d;LjnLB
O00RI3000000000lpiPnh

literal 0
HcmV?d00001

diff --git a/test_files/test_file.vcf.gz.tbi b/test_files/test_file.vcf.gz.tbi
new file mode 100755
index 0000000000000000000000000000000000000000..ddbd1a2d4b92781d99182d5b8fe97ea9d1c0e76c
GIT binary patch
literal 226
zcmb2|=3rp}f&Xj_PR>jWM;W*aKc%E3CL|;<CAn$vGMx&T#oWOw*(1>-=_BFrYLA-Z
zl_MXWo@|eH$_Qi&d7#Z=$iFPFO`&C7YuDi)*DeX{;?v@LeE5v1vr+OCxj80PF-psY
zBW!+same^m@`$&$e8#RKehyhS(e{s`j}%HQLS&A$&ph3q!nQWE#N1Hvr}(pZUAqOO
z?(Y8>@O|-WVRs?vER!4e1L_a{Ieg%Qdmp1_%!Q*D54W;<^6E*kF@!Sst8M|hUmndD
L(hSUCPk{&kmWojr

literal 0
HcmV?d00001

diff --git a/test_files/test_vcf_like.tsv.gz b/test_files/test_vcf_like.tsv.gz
new file mode 100755
index 0000000000000000000000000000000000000000..6a8ea565ea5692b72d555fc249e040a2a5c6e75a
GIT binary patch
literal 1730
zcmV;z20i&7iwFb&00000{{{d;LjnM$2DO??bJ|E0h1Z(DF}o~WdUdz7q!g^8f;}Fi
zQYtHo*d#-h4H;w4{QcZkBOXHiIM52N*ns@`+;bn@lKAuKpSR6x@N2UT-j+Xt_45Du
z;^k%evJBqe7VGWP+v?Z*eDxgsT&|b<@9V|uk`Dj5+N|Yo%@?n$^=7_!qW2rX;VE%f
z?{wIFb9~f%`|*AIzIy+VZw0f-Z8hIMZQhpZ$JgcaYO$Vgm;Zh&*H83U*FQGF{l}|(
zWjkNI&s%8l{C#%+K&t+T0-lF?6pZLGzMoa0{FfvwN`!n~HqWDshj|?Q^_bqWp!hrs
z?&uK(;Y}RIL41?Ze=(Qw9N`KGH*IiHm>+QK&40_6BVY*uYXU|$^qwAA`BWGa4s-BJ
z1Jo*%K+MBx2aNPU%)>{!!pdLKB%}^=aH90(qF<i`7QTU%Z(!-q!4%Y2Q&GoKUz89|
zBtepi6MZS@pcAl!fHeWzKHdRO10F%RyPZDPuaALESJR(Yz)%mw0xlIWGyp4q4l;0T
z)xp@TkNeFqhcn!R>*_0f1FufVF;IX@Qx(jD<P?~l0Y?z9B4BvK()0j4q(p#gu`Do&
z3lpK&S3tlA1w2fdQ(#88!e77=SNcqd1Y#MUsDPWXuK{8izTc%J>j&oG*y?q#3%oid
zUEtM4-33;@iYB7eV}ol<`@vMEgjRHg%flmm3RpnEzZEbt04oUiiGcT`-B%Y?LZ~sJ
zjyr_39lS$#`(rvfJz11Gp`xcZ4*D?XYP&uxx1(KdHNY5luqWUy(4&Jf?BM5JcNp{)
zK7k21Uv6nevnD0E9#}%aS^-0Y!U6(L?FuUhcuPQSj#D_`!W?i4r{voX80mqY1I7|E
zGY8DTeL}CkF0k+yFatM6)(T|cKE?{<;8>UtkV_zo^uQ7V)&w-9goBfCLP2xW=;z?1
zp3p-A8PEH2EWjRdz+vj{Rk%9;1lV*FI=%tMOb^5|JToiI{5qJy4))->`mliSRKQ89
z2NpgR<`=AV!qjy61#7Wra?JEVbW%$o&skrN^9wc~jlQ^lY|*U1*J5EP>IR6e#lo-_
zH$Zgpv?}zMk|=^5G}mAQ^sKMA7T47`@)>XpF78vBGg&id48Rfs)(Xgl9#}!ZDFH1Z
z7uNz0IYv(*rgR6V2{=vq^`R#@Q@W<m09mXDUhUv%z?gpzN}q1Zpf@zE8AfktSOP}x
z;5g|U`2;dBV0m<|514`aN*eollVPscS3$sH2RsXyu3v;a%DJGm<Yd>+Qu@k|pga?_
zcd5oz+%O;LL9fX>bxG3bq>T;hr5;PoLU~2o2elZ4S`I=za)445pCqe~D#Ey-%4I8~
zobfYiglT=GgXy(~8pT?z-D`+e>Z79WOTVGY%GWY&@i$Bn9_}ru_|KU@tzH(ro$45U
zg)qOiN~w*FN{g#KwNWpN-$K2xrY!Yucc4@bPz5woRqsHBP`|d+FcPj*y8})&5O)><
zEA?(qWr-`*?!evNfi%}T5O-EUtJW{A)-2^ltx&%@Q=#6fS_fjD86AMSplY?o88d1v
zukNkWiPd3xnb+N_vS!M;R-t)yiKkvxfo`Q*J^j+wR2HY&no3Zr(<+dlUF9^d6SS*l
zhpsX^0M*s(PyyVi_4-{<AJuoSCIj?pGC=(&=&Eu__U(>3XTKPvrV8&`yLSsMRCx)N
zUX#8?X|oUJIx3JYd6kW_b#y0OoL5!nzM-8tRZNOsDHVMc(7hXJjepw4A9Hj3Km`EQ
z5^<p3JCJ8a2Sx~W(o&-&G*U~%fx2}diBi|PvS;g7QTKJl&nHVaeyh@pI>1VGR9Yg@
zJ9)~`3Gl6@3U&R^g=&xAnF`H-*}emWeg-gf2F&)|nwfp|T>%W807V;r$TDO6P+b*m
z{2@2T4^04Ps_zNF23V~aI#s{5nG#{>TB&wVohp?NP^lc9Do!gPM?1AwsfBuB{`;s<
z1vu?jI646?p?b^~Gy$Bcqd};?=L#QSu5fe$ICX%)&VtL}lcb(~%vlSx+35x>5rw4!
zn(`yCbKg>30cOVh2<#l)S!adl{G@am%`6a+k4mKc=uBoTq5_fmsATRx&EGqk1a>hA
z&^j8#fzcoi6y6=kP_5&=)>OafWvH*?y;k+<3$0eDvPP}ew7IFG*9vvPsMVS#p|e(N
zww$TH$4WN9_{#<u(;2#!)Q6ffI|>cedSCyEaIJrP{D%7f4Vv4=Svo-g03VA81ONa4
Y009360763o02=@U000000000008Vc}d;kCd

literal 0
HcmV?d00001

diff --git a/test_files/test_vcf_like.tsv.gz.tbi b/test_files/test_vcf_like.tsv.gz.tbi
new file mode 100755
index 0000000000000000000000000000000000000000..59c22862ee408b42efb0e303243b7ec3211909d5
GIT binary patch
literal 239
zcmb2|=3rp}f&Xj_PR>jWml)oj-N<{$frm9for!J1;zbLVI3+PzO~??CKHxHi=YYnW
zgK8`_f}T=rCpM?pzMOyF?)|q=*~rk#r7uHIs`=(8{XX0Gc~0fD?bnTL?|eFMu-|3>
zvbi(s>%QH+Ub+6R_{SNp&+i%RciZpReV@m3k_wg3lZf2cya}8Knkr5+Fvz2MNt%Hf
I>_ZR%090pL2><{9

literal 0
HcmV?d00001

diff --git a/test_genome_files/genome_sizes.genome b/test_genome_files/genome_sizes.genome
new file mode 100755
index 0000000..49753b8
--- /dev/null
+++ b/test_genome_files/genome_sizes.genome
@@ -0,0 +1,5 @@
+#chrom	length
+1	249250621
+2	243199373
+3	198022430
+4	191154276