--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/maf_to_fasta-in1.bed	Fri Jul 24 12:35:57 2020 -0400
@@ -0,0 +1,100 @@
+chr22	36937376	36938502	NM_000395.3_cds_13_0_chr22_36937377_f	0	+
+chr22	37723184	37726503	NM_001039141.3_cds_6_0_chr22_37723185_f	0	+
+chr22	37206546	37207803	NM_001051.5_cds_0_0_chr22_37206547_r	0	-
+chr22	32190771	32191352	NM_001098527.3_cds_0_0_chr22_32190772_r	0	-
+chr22	32358071	32358444	NM_001098535.1_cds_0_0_chr22_32358072_f	0	+
+chr22	36265150	36266033	NM_001136540.1_cds_5_0_chr22_36265151_f	0	+
+chr22	36265150	36266033	NM_001136541.1_cds_4_0_chr22_36265151_f	0	+
+chr22	27982220	27983851	NM_001145418.1_cds_0_0_chr22_27982221_r	0	-
+chr22	32190771	32191352	NM_001159545.2_cds_0_0_chr22_32190772_r	0	-
+chr22	32190771	32191352	NM_001159546.2_cds_0_0_chr22_32190772_r	0	-
+chr22	18918315	18918491	NM_001195226.2_cds_3_0_chr22_18918316_r	0	-
+chr22	37206546	37207803	NM_001278687.2_cds_0_0_chr22_37206547_r	0	-
+chr22	17108306	17109820	NM_001289905.1_cds_11_0_chr22_17108307_f	0	+
+chr22	42692889	42693951	NM_001318038.2_cds_0_0_chr22_42692890_r	0	-
+chr22	26026444	26027678	NM_001318245.2_cds_42_0_chr22_26026445_f	0	+
+chr22	21634684	21635644	NM_001331066.1_cds_3_0_chr22_21634685_f	0	+
+chr22	42141151	42141396	NM_001348386.3_cds_2_0_chr22_42141152_r	0	-
+chr22	36265150	36266033	NM_001362927.2_cds_4_0_chr22_36265151_f	0	+
+chr22	32190771	32191352	NM_001364982.1_cds_0_0_chr22_32190772_r	0	-
+chr22	32190771	32191352	NM_001364983.1_cds_0_0_chr22_32190772_r	0	-
+chr22	32190771	32191352	NM_001364984.1_cds_0_0_chr22_32190772_r	0	-
+chr22	32190771	32191352	NM_001364985.1_cds_0_0_chr22_32190772_r	0	-
+chr22	32190771	32191352	NM_001364986.1_cds_0_0_chr22_32190772_r	0	-
+chr22	23573265	23573585	NM_001369906.1_cds_0_0_chr22_23573266_r	0	-
+chr22	27796762	27800543	NM_002430.3_cds_1_0_chr22_27796763_r	0	-
+chr22	36265150	36266033	NM_003661.4_cds_5_0_chr22_36265151_f	0	+
+chr22	21030830	21031812	NM_004173.3_cds_3_0_chr22_21030831_r	0	-
+chr22	42209650	42215305	NM_005650.3_cds_4_0_chr22_42209651_r	0	-
+chr22	46256560	46263322	NM_006071.2_cds_0_0_chr22_46256561_r	0	-
+chr22	32358158	32358444	NM_006604.2_cds_1_0_chr22_32358159_f	0	+
+chr22	38080839	38081679	NM_013356.2_cds_1_0_chr22_38080840_r	0	-
+chr22	46363995	46364251	NM_014246.3_cds_1_0_chr22_46363996_r	0	-
+chr22	46533626	46537170	NM_014246.3_cds_34_0_chr22_46533627_r	0	-
+chr22	17108306	17109820	NM_014339.7_cds_12_0_chr22_17108307_f	0	+
+chr22	36141199	36142058	NM_014349.3_cds_0_0_chr22_36141200_r	0	-
+chr22	49883662	49887178	NM_014838.3_cds_1_0_chr22_49883663_f	0	+
+chr22	17817310	17819129	NM_015241.3_cds_6_0_chr22_17817311_r	0	-
+chr22	18918315	18918491	NM_016335.5_cds_3_0_chr22_18918316_r	0	-
+chr22	42692889	42693951	NM_017436.7_cds_0_0_chr22_42692890_r	0	-
+chr22	37655271	37655684	NM_018957.5_cds_17_0_chr22_37655272_f	0	+
+chr22	23573265	23573585	NM_020070.4_cds_0_0_chr22_23573266_r	0	-
+chr22	29441541	29442122	NM_021026.2_cds_1_0_chr22_29441542_f	0	+
+chr22	29488848	29490703	NM_021076.4_cds_3_0_chr22_29488849_f	0	+
+chr22	35726210	35727194	NM_030642.1_cds_2_0_chr22_35726211_f	0	+
+chr22	36191074	36191912	NM_030643.4_cds_0_0_chr22_36191075_r	0	-
+chr22	36141199	36142058	NM_030644.2_cds_0_0_chr22_36141200_r	0	-
+chr22	17119390	17121127	NM_031890.4_cds_0_0_chr22_17119391_r	0	-
+chr22	26026444	26027678	NM_032608.7_cds_42_0_chr22_26026445_f	0	+
+chr22	22514001	22515630	NM_080740.5_cds_0_0_chr22_22514002_r	0	-
+chr22	50546243	50549951	NM_138433.5_cds_0_0_chr22_50546244_f	0	+
+chr22	36265150	36266033	NM_145343.2_cds_6_0_chr22_36265151_f	0	+
+chr22	36141199	36142058	NM_145639.2_cds_0_0_chr22_36141200_r	0	-
+chr22	36141199	36142058	NM_145640.2_cds_0_0_chr22_36141200_r	0	-
+chr22	36191074	36191912	NM_145660.2_cds_0_0_chr22_36191075_r	0	-
+chr22	21634684	21635266	NM_152612.3_cds_3_0_chr22_21634685_f	0	+
+chr22	31712082	31717291	NM_173566.3_cds_5_0_chr22_31712083_r	0	-
+chr22	42209650	42215305	NM_181492.2_cds_3_0_chr22_42209651_r	0	-
+chr22	36937376	36938502	XM_005261340.3_cds_13_0_chr22_36937377_f	0	+
+chr22	27982220	27983851	XM_005261405.2_cds_0_0_chr22_27982221_r	0	-
+chr22	42692889	42693951	XM_005261644.2_cds_0_0_chr22_42692890_r	0	-
+chr22	42692889	42693951	XM_005261646.4_cds_0_0_chr22_42692890_r	0	-
+chr22	42209650	42215305	XM_005261722.3_cds_4_0_chr22_42209651_r	0	-
+chr22	22646311	22646521	XM_005261815.3_cds_1_0_chr22_22646312_f	0	+
+chr22	22646311	22646521	XM_005261818.2_cds_1_0_chr22_22646312_f	0	+
+chr22	42209650	42215305	XM_006724313.3_cds_4_0_chr22_42209651_r	0	-
+chr22	35726271	35727194	XM_006724321.4_cds_3_0_chr22_35726272_f	0	+
+chr22	46363995	46364251	XM_006724383.3_cds_1_0_chr22_46363996_r	0	-
+chr22	46533626	46537170	XM_006724383.3_cds_34_0_chr22_46533627_r	0	-
+chr22	32190771	32191352	XM_011529826.2_cds_0_0_chr22_32190772_r	0	-
+chr22	32190771	32191352	XM_011529827.3_cds_0_0_chr22_32190772_r	0	-
+chr22	32190771	32191352	XM_011529828.2_cds_0_0_chr22_32190772_r	0	-
+chr22	32190771	32191352	XM_011529832.2_cds_0_0_chr22_32190772_r	0	-
+chr22	42209650	42215305	XM_011530353.2_cds_4_0_chr22_42209651_r	0	-
+chr22	42209650	42215305	XM_011530354.2_cds_3_0_chr22_42209651_r	0	-
+chr22	26026444	26027678	XM_011530458.2_cds_43_0_chr22_26026445_f	0	+
+chr22	26026444	26027678	XM_011530459.2_cds_43_0_chr22_26026445_f	0	+
+chr22	26026444	26027678	XM_011530460.2_cds_42_0_chr22_26026445_f	0	+
+chr22	26026444	26027678	XM_011530461.2_cds_43_0_chr22_26026445_f	0	+
+chr22	26026444	26027678	XM_011530464.2_cds_43_0_chr22_26026445_f	0	+
+chr22	26026444	26027678	XM_011530465.2_cds_42_0_chr22_26026445_f	0	+
+chr22	36265199	36266033	XM_011530478.2_cds_5_0_chr22_36265200_f	0	+
+chr22	46533626	46537170	XM_011530553.1_cds_16_0_chr22_46533627_r	0	-
+chr22	46363995	46364251	XM_011530554.2_cds_1_0_chr22_46363996_r	0	-
+chr22	46363995	46364251	XM_011530555.2_cds_1_0_chr22_46363996_r	0	-
+chr22	17119390	17121127	XM_011546124.2_cds_1_0_chr22_17119391_r	0	-
+chr22	32358153	32358611	XM_017028534.1_cds_1_0_chr22_32358154_f	0	+
+chr22	35726284	35727194	XM_017028945.2_cds_2_0_chr22_35726285_f	0	+
+chr22	26026444	26027678	XM_017029012.1_cds_43_0_chr22_26026445_f	0	+
+chr22	26026444	26027678	XM_017029013.1_cds_43_0_chr22_26026445_f	0	+
+chr22	26026444	26027678	XM_017029014.1_cds_43_0_chr22_26026445_f	0	+
+chr22	26026444	26027678	XM_017029015.1_cds_42_0_chr22_26026445_f	0	+
+chr22	26026444	26027678	XM_017029016.1_cds_31_0_chr22_26026445_f	0	+
+chr22	26026444	26027678	XM_017029017.1_cds_41_0_chr22_26026445_f	0	+
+chr22	18846931	18848320	XM_017029167.2_cds_0_0_chr22_18846932_f	0	+
+chr22	23394179	23394792	XM_017029168.1_cds_3_0_chr22_23394180_f	0	+
+chr22	23394222	23394792	XM_017029169.1_cds_2_0_chr22_23394223_f	0	+
+chr22	50433133	50434498	XM_017029177.1_cds_0_0_chr22_50433134_r	0	-
+chr22	50433133	50434498	XM_017029178.1_cds_0_0_chr22_50433134_r	0	-
+chr22	36191074	36191842	XM_024452274.1_cds_0_0_chr22_36191075_r	0	-
+chr22	49883662	49887178	XM_024452312.1_cds_1_0_chr22_49883663_f	0	+