--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/maf_to_fasta-in2.bed	Fri Aug 21 15:10:13 2020 -0400
@@ -0,0 +1,250 @@
+chr22	17904727	18001180	ENST00000424046.1	0	-	17904727	17906812	0	3	112,338,92,	0,1821,96361,
+chr22	17980867	17980961	ENST00000385046.1	0	-	17980867	17980867	0	1	94,	0,
+chr22	17983204	17983619	ENST00000429618.1	0	-	17983204	17983204	0	2	83,278,	0,137,
+chr22	18004269	18007308	ENST00000441167.1	0	-	18004269	18004269	0	2	2346,147,	0,2892,
+chr22	18019213	18020200	ENST00000411920.1	0	+	18019213	18019213	0	3	198,66,87,	0,522,900,
+chr22	18029384	18037968	ENST00000443243.1	0	+	18029384	18029384	0	2	170,2209,	0,6375,
+chr22	18076526	18077797	ENST00000426483.1	0	-	18076526	18076526	0	2	536,269,	0,1002,
+chr22	18077185	18078884	ENST00000607927.1	0	-	18077185	18077185	0	1	1699,	0,
+chr22	18077919	18091019	ENST00000610387.4	0	+	18078376	18088075	0	5	128,311,141,296,3048,	0,376,1954,5517,10052,
+chr22	18077922	18105396	ENST00000329627.11	0	+	18078376	18088075	0	6	125,311,141,296,147,17425,	0,373,1951,5514,7189,10049,
+chr22	18078007	18088460	ENST00000399744.7	0	+	18078376	18088075	0	5	599,141,296,147,489,	0,1866,5429,7104,9964,
+chr22	18078014	18131138	ENST00000474897.5	0	+	18078376	18121677	0	6	592,141,223,149,681,296,	0,1859,43464,46141,48339,52828,
+chr22	18078054	18078775	ENST00000622035.1	0	-	18078054	18078054	0	1	721,	0,
+chr22	18078376	18088119	ENST00000428061.2	0	+	18078376	18088075	0	4	230,141,296,148,	0,1497,5060,9595,
+chr22	18081465	18081675	ENST00000427227.2	0	-	18081465	18081465	0	1	210,	0,
+chr22	18101611	18101888	ENST00000450866.1	0	+	18101611	18101611	0	1	277,	0,
+chr22	18102456	18103649	ENST00000446487.1	0	-	18102456	18102456	0	2	338,193,	0,1000,
+chr22	18110330	18124268	ENST00000426208.5	0	+	18121673	18124268	0	3	246,223,113,	0,11148,13825,
+chr22	18110686	18131154	ENST00000316027.10	0	+	18121673	18131136	0	5	153,223,149,681,312,	0,10792,13469,15667,20156,
+chr22	18110758	18131154	ENST00000623543.1	0	-	18110758	18110758	0	1	20396,	0,
+chr22	18110808	18131732	ENST00000330423.8	0	+	18110865	18131136	0	5	60,223,149,681,890,	0,10670,13347,15545,20034,
+chr22	18121106	18131117	ENST00000416740.1	0	+	18121403	18131117	0	4	595,149,681,275,	0,3049,5247,9736,
+chr22	18126706	18146554	ENST00000608634.1	0	+	18126706	18145989	0	3	328,164,899,	0,4136,18949,
+chr22	18150169	18177397	ENST00000215794.8	0	+	18157663	18176817	0	11	53,263,97,146,80,147,96,168,132,50,626,	0,7388,10002,11620,17085,17720,19674,20583,22980,23623,26602,
+chr22	18178037	18205915	ENST00000434390.1	0	-	18178037	18178037	0	9	428,957,34,62,66,87,25,59,141,	0,5072,10585,11084,13145,18119,21152,21645,27737,
+chr22	18340144	18345899	ENST00000617623.1	0	+	18340144	18340144	0	7	172,137,188,127,113,114,147,	0,695,4347,4767,4996,5190,5608,
+chr22	18361819	18386597	ENST00000619172.5	0	-	18361819	18361819	0	12	438,155,41,73,2323,34,62,66,87,25,59,212,	0,5081,5698,5965,6571,11103,11602,13664,18636,21667,22160,24566,
+chr22	18361829	18386526	ENST00000618517.4	0	-	18361829	18361829	0	9	428,957,34,62,66,87,25,59,141,	0,5071,11093,11592,13654,18626,21657,22150,24556,
+chr22	18370584	18386480	ENST00000613790.4	0	-	18370584	18370584	0	8	129,34,62,66,87,25,59,95,	0,2338,2837,4899,9871,12902,13395,15801,
+chr22	18370665	18391105	ENST00000615974.1	0	-	18370665	18370665	0	9	48,34,62,66,87,25,59,59,287,	0,2257,2756,4818,9790,12821,13314,19243,20153,
+chr22	18374105	18375689	ENST00000622906.1	0	+	18374105	18374105	0	2	116,259,	0,1325,
+chr22	18400406	18404206	ENST00000612861.1	0	-	18400406	18400406	0	1	3800,	0,
+chr22	18422243	18500594	ENST00000624459.2	0	+	18422243	18422243	0	12	104,59,25,87,66,62,34,2041,73,41,155,439,	0,2733,3260,6231,64895,66961,67488,69742,72316,72615,73118,77912,
+chr22	18424976	18490146	ENST00000624001.2	0	+	18424976	18424976	0	6	59,25,87,66,62,415,	0,527,3498,62162,64228,64755,
+chr22	18486998	18488582	ENST00000614584.1	0	-	18486998	18486998	0	2	259,116,	0,1468,
+chr22	18487125	18489905	ENST00000615181.4	0	+	18487125	18487125	0	3	79,62,174,	0,2079,2606,
+chr22	18487868	18491247	ENST00000620909.1	0	-	18487868	18487868	0	2	715,105,	0,3274,
+chr22	18501793	18512187	ENST00000621762.1	0	-	18501793	18501793	0	2	56,302,	0,10092,
+chr22	18516343	18518161	ENST00000619998.1	0	-	18516500	18517897	0	6	304,114,113,128,210,99,	0,608,803,1018,1378,1719,
+chr22	18524619	18524935	ENST00000618466.1	0	+	18524619	18524619	0	1	316,	0,
+chr22	18527156	18527626	ENST00000359859.4	0	+	18527156	18527156	0	1	470,	0,
+chr22	18527801	18530571	ENST00000614395.4	0	+	18527801	18527801	0	5	475,535,57,403,416,	0,757,1639,1804,2354,
+chr22	18527801	18530573	ENST00000612978.5	0	+	18527980	18530459	0	9	475,124,51,75,57,119,73,41,319,	0,757,1015,1217,1639,1804,2134,2354,2453,
+chr22	18528946	18530222	ENST00000620199.4	0	+	18528946	18528946	0	5	147,57,119,73,67,	0,494,659,989,1209,
+chr22	18529041	18530178	ENST00000613577.4	0	+	18529041	18530178	0	6	52,57,84,65,73,23,	0,399,564,750,894,1114,
+chr22	18529065	18530204	ENST00000621725.4	0	+	18529065	18529065	0	4	28,57,119,269,	0,375,540,870,
+chr22	18529408	18530573	ENST00000618859.1	0	+	18529408	18529408	0	4	89,119,261,319,	0,197,527,846,
+chr22	18529809	18530459	ENST00000613597.1	0	+	18529809	18530459	0	4	47,73,41,205,	0,126,346,445,
+chr22	18533645	18537791	ENST00000610959.4	0	-	18533645	18533645	0	3	408,84,1933,	0,1599,2213,
+chr22	18533655	18552527	ENST00000652586.1	0	-	18533655	18533655	0	17	398,84,90,159,121,126,105,110,71,73,71,130,128,108,152,158,55,	0,1589,2203,2994,3636,4777,4984,5572,6746,6917,10011,10996,13590,14355,14662,15014,18817,
+chr22	18533656	18537865	ENST00000619742.4	0	-	18533656	18533656	0	4	397,84,90,1216,	0,1588,2202,2993,
+chr22	18533656	18548353	ENST00000617243.4	0	-	18533656	18533656	0	14	397,84,90,763,126,105,110,71,73,71,130,176,108,36,	0,1588,2202,2993,4776,4983,5571,6745,6916,10010,10995,13589,14354,14661,
+chr22	18533670	18548828	ENST00000618794.4	0	-	18533670	18533670	0	15	383,84,90,763,126,105,110,71,73,71,130,128,108,152,159,	0,1574,2188,2979,4762,4969,5557,6731,6902,9996,10981,13575,14340,14647,14999,
+chr22	18534004	18548798	ENST00000612579.4	0	-	18534004	18534004	0	16	49,84,90,159,118,126,105,110,71,73,71,130,128,108,152,129,	0,1240,1854,2645,3290,4428,4635,5223,6397,6568,9662,10647,13241,14006,14313,14665,
+chr22	18538022	18574700	ENST00000612500.4	0	-	18538022	18538022	0	13	536,105,110,71,73,71,130,128,108,152,158,101,126,	0,617,1205,2379,2550,5644,6629,9223,9988,10295,10647,14450,36552,
+chr22	18538055	18577968	ENST00000611748.1	0	-	18538055	18538055	0	13	503,105,110,71,73,71,130,128,108,152,158,101,196,	0,584,1172,2346,2517,5611,6596,9190,9955,10262,10614,14417,39717,
+chr22	18548010	18548770	ENST00000616531.1	0	-	18548010	18548010	0	2	459,101,	0,659,
+chr22	18605354	18605497	ENST00000614296.1	0	+	18605354	18605354	0	1	143,	0,
+chr22	18605801	18606102	ENST00000410698.2	0	-	18605801	18605801	0	1	301,	0,
+chr22	18605814	18611919	ENST00000619918.1	0	-	18606514	18611434	0	1	6105,	0,
+chr22	18615580	18615900	ENST00000611762.1	0	+	18615580	18615580	0	1	320,	0,
+chr22	18623338	18625289	ENST00000611186.1	0	-	18623338	18623338	0	4	173,164,145,276,	0,637,1289,1675,
+chr22	18633983	18634682	ENST00000652395.1	0	+	18633983	18634682	0	1	699,	0,
+chr22	18636444	18638405	ENST00000611168.1	0	-	18636444	18636444	0	5	361,69,65,171,168,	0,467,879,1047,1793,
+chr22	18650022	18653617	ENST00000611403.1	0	-	18650022	18650022	0	1	3595,	0,
+chr22	18715814	18719341	ENST00000619065.1	0	+	18715814	18715814	0	1	3527,	0,
+chr22	18733913	18757894	ENST00000342888.3	0	+	18733913	18733913	0	9	141,59,25,87,66,62,34,957,428,	0,2118,2645,5616,10596,12660,13187,17955,23553,
+chr22	18756347	18757906	ENST00000611876.1	0	+	18756347	18756347	0	1	1559,	0,
+chr22	18773664	18805479	ENST00000412448.5	0	-	18773664	18773664	0	15	304,114,113,127,210,137,150,158,193,168,77,87,72,379,51,	0,608,803,1018,1377,5065,5725,7924,8474,17394,18108,18303,18597,20748,31764,
+chr22	18773824	18791223	ENST00000453783.2	0	-	18773824	18773824	0	12	144,114,113,127,191,137,150,158,193,87,135,165,	0,448,643,858,1217,4905,5565,7764,8314,13706,13920,17234,
+chr22	18794413	18794804	ENST00000437537.1	0	-	18794413	18794413	0	1	391,	0,
+chr22	18794530	18843399	ENST00000445651.1	0	-	18794530	18794530	0	2	261,107,	0,48762,
+chr22	18794597	18825001	ENST00000430306.1	0	-	18794597	18794597	0	2	194,74,	0,30330,
+chr22	18833693	18834438	ENST00000428850.2	0	+	18833693	18833693	0	1	745,	0,
+chr22	18846810	18856684	ENST00000419447.5	0	+	18846810	18846810	0	5	1516,207,106,129,110,	0,4826,6839,8979,9764,
+chr22	18846931	18848320	ENST00000342005.5	0	+	18846931	18846931	0	1	1389,	0,
+chr22	18850117	18861049	ENST00000412938.5	0	+	18850117	18850117	0	6	1726,376,106,129,915,2668,	0,2101,3532,5672,6457,8264,
+chr22	18852875	18854933	ENST00000416498.1	0	+	18852875	18852875	0	3	67,106,186,	0,774,1872,
+chr22	18855620	18858640	ENST00000511549.1	0	-	18855620	18855620	0	4	163,106,135,140,	0,639,1690,2880,
+chr22	18873542	18894407	ENST00000614596.2	0	-	18873542	18873542	0	8	123,34,62,66,87,25,59,79,	0,2336,2835,4896,9870,12903,13396,20786,
+chr22	18883501	18884682	ENST00000623570.1	0	-	18883501	18883501	0	1	1181,	0,
+chr22	18906027	18912088	ENST00000413981.5	0	+	18910923	18911689	0	5	87,161,101,141,549,	0,537,4144,4860,5512,
+chr22	18906237	18947732	ENST00000638240.1	0	+	18906374	18939702	0	6	247,161,101,141,77,942,	0,327,3934,4650,33435,40553,
+chr22	18906319	18914238	ENST00000331444.11	0	+	18906374	18911689	0	5	165,161,101,141,2699,	0,245,3852,4568,5220,
+chr22	18906324	18914238	ENST00000483718.5	0	+	18906374	18910232	0	5	143,161,101,141,2699,	0,240,3847,4563,5215,
+chr22	18906350	18912082	ENST00000427407.5	0	+	18906374	18910270	0	6	134,161,119,101,141,543,	0,214,3629,3821,4537,5189,
+chr22	18906352	18908269	ENST00000608842.1	0	+	18906374	18906889	0	2	132,1705,	0,212,
+chr22	18906354	18912087	ENST00000480608.5	0	+	18906374	18906889	0	5	130,522,94,141,548,	0,210,3824,4533,5185,
+chr22	18906780	18910389	ENST00000477156.1	0	+	18906780	18906780	0	2	306,218,	0,3391,
+chr22	18908662	18912078	ENST00000436645.1	0	+	18908662	18908662	0	4	31,101,141,539,	0,1509,2225,2877,
+chr22	18912776	18936553	ENST00000610940.4	0	-	18913174	18936287	0	15	586,89,99,176,147,93,82,80,117,65,150,35,209,313,164,	0,661,4113,5539,6674,6929,8565,9548,10040,10338,12274,12911,18213,23238,23613,
+chr22	18912780	18936295	ENST00000491604.5	0	-	18912780	18912780	0	13	582,89,99,176,147,93,1063,117,65,150,35,209,281,	0,657,4109,5535,6670,6925,8561,10036,10334,12270,12907,18209,23234,
+chr22	18912780	18936296	ENST00000420436.5	0	-	18913174	18931147	0	14	582,89,99,176,147,93,82,80,117,65,150,35,192,127,	0,657,4109,5535,6670,6925,8561,9544,10036,10334,12270,12907,18209,23389,
+chr22	18912781	18921574	ENST00000313755.9	0	-	18912781	18912781	0	6	581,89,99,176,147,1869,	0,656,4108,5534,6669,6924,
+chr22	18912781	18924002	ENST00000429300.5	0	-	18912781	18912781	0	9	581,89,99,176,181,93,82,80,1186,	0,656,4108,5534,6669,6924,8560,9543,10035,
+chr22	18912781	18936142	ENST00000482858.5	0	-	18912781	18912781	0	11	581,89,99,176,147,2699,363,150,35,209,128,	0,656,4108,5534,6669,6924,10035,12269,12906,18208,23233,
+chr22	18912781	18936451	ENST00000334029.6	0	-	18913174	18931147	0	14	581,89,99,176,147,93,82,80,117,65,150,35,209,62,	0,656,4108,5534,6669,6924,8560,9543,10035,10333,12269,12906,18208,23608,
+chr22	18912781	18936553	ENST00000357068.10	0	-	18913174	18936287	0	14	581,89,99,176,147,93,82,80,117,65,150,35,209,539,	0,656,4108,5534,6669,6924,8560,9543,10035,10333,12269,12906,18208,23233,
+chr22	18914529	18921554	ENST00000609229.1	0	-	18914529	18914529	0	3	2459,176,2104,	0,3786,4921,
+chr22	18919555	18921539	ENST00000446371.1	0	-	18919555	18919555	0	2	243,198,	0,1786,
+chr22	18921380	18936142	ENST00000438924.5	0	-	18921380	18936142	0	6	43,80,117,150,35,128,	0,944,1436,3670,4307,14634,
+chr22	18922245	18923310	ENST00000399694.1	0	-	18922245	18922245	0	3	159,117,196,	0,571,869,
+chr22	18922371	18934828	ENST00000450579.1	0	-	18922371	18930994	0	7	33,117,65,150,35,127,67,	0,445,743,2679,3316,8618,12390,
+chr22	18922879	18936266	ENST00000457083.1	0	-	18922879	18936266	0	4	54,150,35,252,	0,2171,2808,13135,
+chr22	18924724	18931110	ENST00000496625.1	0	-	18924724	18924724	0	3	476,35,121,	0,963,6265,
+chr22	18936410	18947741	ENST00000640084.1	0	+	18936410	18936410	0	4	238,116,77,951,	0,941,3262,10380,
+chr22	18939445	18947692	ENST00000638287.1	0	+	18939445	18939445	0	2	312,902,	0,7345,
+chr22	18945122	18946971	ENST00000623496.1	0	+	18945122	18945122	0	2	47,181,	0,1668,
+chr22	18951933	18959512	ENST00000624224.1	0	-	18951933	18951933	0	1	7579,	0,
+chr22	18970513	18994628	ENST00000438934.5	0	+	18970513	18970513	0	5	145,144,105,49,5049,	0,17243,17577,18903,19066,
+chr22	18970524	19031242	ENST00000440005.6	0	+	18970524	18970524	0	6	134,144,205,201,154,461,	0,17232,20195,21292,43828,60257,
+chr22	18970582	18990883	ENST00000421572.1	0	+	18970582	18970582	0	4	76,184,144,164,	0,15253,17174,20137,
+chr22	18980694	18981325	ENST00000636418.1	0	-	18980694	18980694	0	2	86,90,	0,541,
+chr22	18985835	18994501	ENST00000399539.4	0	+	18985835	18985835	0	5	184,144,205,201,128,	0,1921,4884,5981,8538,
+chr22	18989918	19020248	ENST00000609630.2	0	+	18989918	18989918	0	7	46,205,201,59,107,154,2952,	0,801,1898,12948,15917,24434,27378,
+chr22	18997137	18997595	ENST00000604539.1	0	-	18997137	18997137	0	1	458,	0,
+chr22	18998273	19014786	ENST00000424407.1	0	+	18998273	18998273	0	5	256,59,110,154,189,	0,4593,7559,16079,16324,
+chr22	19014352	19014506	ENST00000637415.1	0	+	19014352	19014352	0	1	154,	0,
+chr22	19018042	19018916	ENST00000603208.1	0	-	19018042	19018042	0	1	874,	0,
+chr22	19023055	19023550	ENST00000609839.1	0	+	19023055	19023055	0	1	495,	0,
+chr22	19029523	19031242	ENST00000652053.1	0	+	19029523	19030221	0	1	1719,	0,
+chr22	19031563	19034564	ENST00000481698.1	0	-	19031563	19031563	0	8	120,87,158,67,107,170,160,36,	0,433,635,902,1270,1480,2228,2965,
+chr22	19036281	19122454	ENST00000537045.5	0	-	19038864	19122206	0	9	2840,237,153,204,177,77,220,126,327,	0,4776,5525,12158,20704,26920,28566,31818,85846,
+chr22	19036281	19122454	ENST00000545799.5	0	-	19038864	19122206	0	11	2840,237,153,204,177,77,211,5,130,123,327,	0,4776,5525,12158,20704,26920,28566,28903,31814,53086,85846,
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+chr22	19565202	19566839	ENST00000629028.1	0	-	19565202	19565202	0	1	1637,	0,
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+chr22	19720341	19721869	ENST00000480423.5	0	+	19720341	19720341	0	4	113,118,102,230,	0,207,426,1298,
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+chr22	19722944	19724771	ENST00000366425.3	0	+	19723569	19724464	0	2	635,918,	0,909,
+chr22	19756702	19767334	ENST00000332710.8	0	+	19759643	19766867	0	9	43,120,376,102,172,156,68,101,946,	0,2855,4202,6538,7452,8255,9055,9199,9686,
+chr22	19756702	19779546	ENST00000329705.11	0	+	19759643	19779407	0	9	43,120,376,102,172,156,68,101,327,	0,2855,4202,6538,7452,8255,9055,9199,22517,
+chr22	19756702	19783593	ENST00000359500.7	0	+	19759643	19783022	0	10	43,120,376,102,172,156,68,101,120,280,	0,2855,4202,6538,7452,8255,9055,9199,26210,26611,
+chr22	19760820	19767332	ENST00000649276.1	0	+	19760843	19766867	0	7	460,102,172,156,68,101,944,	0,2420,3334,4137,4937,5081,5568,
+chr22	19761196	19763702	ENST00000475303.1	0	+	19761196	19761196	0	2	84,462,	0,2044,
+chr22	19765078	19766327	ENST00000484336.1	0	+	19765078	19765078	0	3	35,68,426,	0,679,823,
+chr22	19783222	19854874	ENST00000329517.11	0	-	19788708	19821355	0	8	5738,216,99,163,126,148,97,55,	0,18778,23436,29062,37375,38005,71220,71597,
+chr22	19788414	19854843	ENST00000403325.5	0	-	19788708	19821355	0	7	546,216,99,163,126,148,401,	0,13586,18244,23870,32183,32813,66028,
+chr22	19788417	19854939	ENST00000405009.5	0	-	19788617	19821355	0	8	209,114,99,163,126,148,97,120,	0,13685,18241,23867,32180,32810,66025,66402,
+chr22	19788463	19854806	ENST00000460402.5	0	-	19788463	19788463	0	6	497,216,99,163,97,125,	0,13537,18195,23821,65979,66218,
+chr22	19792293	19793094	ENST00000424559.2	0	+	19792293	19792293	0	1	801,	0,
+chr22	19801998	19854816	ENST00000481086.1	0	-	19801998	19801998	0	4	218,99,163,374,	0,4660,10286,52444,
+chr22	19812294	19854843	ENST00000453108.1	0	-	19812294	19821355	0	3	153,148,401,	0,8933,42148,
+chr22	19846137	19854896	ENST00000407472.5	0	-	19851166	19852261	0	3	6349,97,77,	0,8305,8682,
+chr22	19846145	19854863	ENST00000484072.5	0	-	19846145	19846145	0	3	1244,97,44,	0,8297,8674,
+chr22	19846145	19854874	ENST00000328554.9	0	-	19851166	19852261	0	3	6341,97,215,	0,8297,8514,
+chr22	19846145	19854886	ENST00000405640.1	0	-	19851166	19852261	0	2	6341,444,	0,8297,
+chr22	19851988	19854816	ENST00000416337.1	0	-	19851988	19852261	0	3	498,97,135,	0,2454,2693,
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