--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/cf-gene2exon.dat	Sat Feb 21 16:33:42 2015 +0100
@@ -0,0 +1,325 @@
+chr1	147962006	147962580	NM_005997	0	-
+chr1	147963549	147963694	NM_005997	0	-
+chr1	147969865	147970042	NM_005997	0	-
+chr1	147971054	147971169	NM_005997	0	-
+chr1	147971346	147971499	NM_005997	0	-
+chr1	147975553	147975713	NM_005997	0	-
+chr1	147984101	147984630	BC007833	0	+
+chr1	148009796	148009828	BC007833	0	+
+chr1	148012868	148012949	BC007833	0	+
+chr1	148017219	148017350	BC007833	0	+
+chr1	148017796	148017914	BC007833	0	+
+chr1	148018099	148018252	BC007833	0	+
+chr1	148019745	148020045	BC007833	0	+
+chr1	148022106	148022312	BC007833	0	+
+chr1	148023730	148023814	BC007833	0	+
+chr1	148024678	148024727	BC007833	0	+
+chr1	148025503	148025588	BC007833	0	+
+chr1	148027986	148028116	BC007833	0	+
+chr1	148032468	148032514	BC007833	0	+
+chr1	148033411	148035079	BC007833	0	+
+chr1	148077485	148078582	NM_002651	0	-
+chr1	148079566	148079687	NM_002651	0	-
+chr1	148079957	148080090	NM_002651	0	-
+chr1	148084356	148084622	NM_002651	0	-
+chr1	148087392	148087516	NM_002651	0	-
+chr1	148087742	148087847	NM_002651	0	-
+chr1	148089089	148089199	NM_002651	0	-
+chr1	148091684	148091912	NM_002651	0	-
+chr1	148093122	148093350	NM_002651	0	-
+chr1	148095759	148095804	NM_002651	0	-
+chr1	148101121	148102058	NM_002651	0	-
+chr1	148111720	148111797	NM_002651	0	-
+chr1	148185113	148185276	NM_002796	0	+
+chr1	148185529	148185736	NM_002796	0	+
+chr1	148185990	148186137	NM_002796	0	+
+chr1	148186312	148186394	NM_002796	0	+
+chr1	148186787	148186904	NM_002796	0	+
+chr1	148187090	148187179	NM_002796	0	+
+chr1	148187365	148187485	NM_002796	0	+
+chr2	118288484	118288668	NM_006773	0	+
+chr2	118291249	118291534	NM_006773	0	+
+chr2	118293454	118293598	NM_006773	0	+
+chr2	118294966	118295102	NM_006773	0	+
+chr2	118295455	118295556	NM_006773	0	+
+chr2	118295667	118295867	NM_006773	0	+
+chr2	118295952	118296067	NM_006773	0	+
+chr2	118298374	118298514	NM_006773	0	+
+chr2	118298745	118298907	NM_006773	0	+
+chr2	118299252	118299405	NM_006773	0	+
+chr2	118300074	118300188	NM_006773	0	+
+chr2	118302754	118302811	NM_006773	0	+
+chr2	118303094	118303272	NM_006773	0	+
+chr2	118304387	118306183	NM_006773	0	+
+chr2	118389378	118390700	BC005078	0	-
+chr2	220108603	220109267	NM_001927	0	+
+chr2	220110321	220110382	NM_001927	0	+
+chr2	220110477	220110573	NM_001927	0	+
+chr2	220110721	220110883	NM_001927	0	+
+chr2	220111054	220111180	NM_001927	0	+
+chr2	220111566	220111787	NM_001927	0	+
+chr2	220114003	220114047	NM_001927	0	+
+chr2	220115889	220115972	NM_001927	0	+
+chr2	220116175	220116964	NM_001927	0	+
+chr2	220229182	220230869	NM_024536	0	-
+chr2	220231172	220231352	NM_024536	0	-
+chr2	220231842	220232416	NM_024536	0	-
+chr2	220233451	220233943	NM_024536	0	-
+chr5	131170738	131170850	AF099740	0	-
+chr5	131182331	131182455	AF099740	0	-
+chr5	131214855	131214975	AF099740	0	-
+chr5	131218345	131218426	AF099740	0	-
+chr5	131275406	131275471	AF099740	0	-
+chr5	131280477	131280517	AF099740	0	-
+chr5	131285413	131285533	AF099740	0	-
+chr5	131297104	131297233	AF099740	0	-
+chr5	131306226	131306287	AF099740	0	-
+chr5	131308256	131308344	AF099740	0	-
+chr5	131308747	131308841	AF099740	0	-
+chr5	131311175	131311254	AF099740	0	-
+chr5	131323127	131323199	AF099740	0	-
+chr5	131324111	131324213	AF099740	0	-
+chr5	131326126	131326270	AF099740	0	-
+chr5	131330007	131330124	AF099740	0	-
+chr5	131331531	131331620	AF099740	0	-
+chr5	131333719	131333792	AF099740	0	-
+chr5	131335141	131335237	AF099740	0	-
+chr5	131336315	131336450	AF099740	0	-
+chr5	131336857	131336992	AF099740	0	-
+chr5	131338349	131338427	AF099740	0	-
+chr5	131340239	131340313	AF099740	0	-
+chr5	131348998	131349050	AF099740	0	-
+chr5	131350413	131350446	AF099740	0	-
+chr5	131351639	131351818	AF099740	0	-
+chr5	131352396	131352496	AF099740	0	-
+chr5	131352998	131353100	AF099740	0	-
+chr5	131353691	131353756	AF099740	0	-
+chr5	131354444	131354559	AF099740	0	-
+chr5	131357622	131357870	AF099740	0	-
+chr5	131424245	131424460	NM_000588	0	+
+chr5	131424558	131424600	NM_000588	0	+
+chr5	131425903	131425993	NM_000588	0	+
+chr5	131426117	131426159	NM_000588	0	+
+chr5	131426260	131426795	NM_000588	0	+
+chr5	131556201	131556672	NM_004199	0	-
+chr5	131558517	131558614	NM_004199	0	-
+chr5	131559003	131559072	NM_004199	0	-
+chr5	131561797	131561863	NM_004199	0	-
+chr5	131562470	131562524	NM_004199	0	-
+chr5	131567339	131567439	NM_004199	0	-
+chr5	131567673	131567744	NM_004199	0	-
+chr5	131571299	131571476	NM_004199	0	-
+chr5	131572729	131572923	NM_004199	0	-
+chr5	131573875	131574115	NM_004199	0	-
+chr5	131577507	131577645	NM_004199	0	-
+chr5	131580788	131580940	NM_004199	0	-
+chr5	131581343	131581440	NM_004199	0	-
+chr5	131582136	131582236	NM_004199	0	-
+chr5	131590288	131590458	NM_004199	0	-
+chr5	131621285	131621419	NM_003687	0	+
+chr5	131626200	131626352	NM_003687	0	+
+chr5	131630055	131630137	NM_003687	0	+
+chr5	131634506	131634685	NM_003687	0	+
+chr5	131634894	131635058	NM_003687	0	+
+chr5	131635382	131635500	NM_003687	0	+
+chr5	131635616	131637046	NM_003687	0	+
+chr6	108298214	108299744	NM_007214	0	-
+chr6	108300704	108300809	NM_007214	0	-
+chr6	108304460	108304559	NM_007214	0	-
+chr6	108309045	108309147	NM_007214	0	-
+chr6	108310884	108311043	NM_007214	0	-
+chr6	108321378	108321552	NM_007214	0	-
+chr6	108321734	108321794	NM_007214	0	-
+chr6	108325545	108325628	NM_007214	0	-
+chr6	108329266	108329414	NM_007214	0	-
+chr6	108330740	108330895	NM_007214	0	-
+chr6	108332525	108332618	NM_007214	0	-
+chr6	108334344	108334477	NM_007214	0	-
+chr6	108334579	108334674	NM_007214	0	-
+chr6	108336823	108336932	NM_007214	0	-
+chr6	108339242	108339293	NM_007214	0	-
+chr6	108340612	108340671	NM_007214	0	-
+chr6	108341262	108341324	NM_007214	0	-
+chr6	108349693	108349806	NM_007214	0	-
+chr6	108352714	108352829	NM_007214	0	-
+chr6	108357311	108357411	NM_007214	0	-
+chr6	108385782	108386086	NM_007214	0	-
+chr6	108593954	108594687	NM_003269	0	+
+chr6	108599354	108599500	NM_003269	0	+
+chr6	108602732	108602820	NM_003269	0	+
+chr6	108604399	108604635	NM_003269	0	+
+chr6	108605991	108606138	NM_003269	0	+
+chr6	108608219	108608316	NM_003269	0	+
+chr6	108608703	108608853	NM_003269	0	+
+chr6	108609442	108609548	NM_003269	0	+
+chr6	108615197	108616704	NM_003269	0	+
+chr6	108639410	108640151	NM_152827	0	-
+chr6	108642394	108642519	NM_152827	0	-
+chr6	108688656	108689143	NM_152827	0	-
+chr6	108722790	108723115	NM_145315	0	+
+chr6	108751721	108751945	NM_145315	0	+
+chr6	108774884	108774936	NM_145315	0	+
+chr6	108783550	108783652	NM_145315	0	+
+chr6	108784586	108784717	NM_145315	0	+
+chr6	108794129	108794229	NM_145315	0	+
+chr6	108829892	108829951	NM_145315	0	+
+chr6	108875109	108875192	NM_145315	0	+
+chr6	108904760	108904831	NM_145315	0	+
+chr6	108905087	108905188	NM_145315	0	+
+chr6	108938107	108938248	NM_145315	0	+
+chr6	108947592	108947706	NM_145315	0	+
+chr6	108950192	108950942	NM_145315	0	+
+chr7	113320332	113320617	AK131266	0	+
+chr7	113522024	113522115	AK131266	0	+
+chr7	113660507	113660685	AK131266	0	+
+chr7	113768622	113768712	AK131266	0	+
+chr7	113772331	113772389	AK131266	0	+
+chr7	113804812	113804887	AK131266	0	+
+chr7	113862545	113862683	AK131266	0	+
+chr7	113863597	113863648	AK131266	0	+
+chr7	113863810	113864011	AK131266	0	+
+chr7	113865533	113865711	AK131266	0	+
+chr7	113876415	113876629	AK131266	0	+
+chr7	113878690	113878795	AK131266	0	+
+chr7	113886208	113886296	AK131266	0	+
+chr7	113887931	113888015	AK131266	0	+
+chr7	113893361	113893438	AK131266	0	+
+chr7	113893577	113893679	AK131266	0	+
+chr7	113896070	113896192	AK131266	0	+
+chr7	113897455	113897525	AK131266	0	+
+chr7	113898278	113898442	AK131266	0	+
+chr7	113923787	113924911	AK131266	0	+
+chr7	116511232	116512389	NM_003391	0	-
+chr7	116531616	116531881	NM_003391	0	-
+chr7	116549075	116549353	NM_003391	0	-
+chr7	116554571	116554798	NM_003391	0	-
+chr7	116556911	116557294	NM_003391	0	-
+chr7	116713967	116714152	NM_000492	0	+
+chr7	116738257	116738368	NM_000492	0	+
+chr7	116743038	116743147	NM_000492	0	+
+chr7	116764903	116765119	NM_000492	0	+
+chr7	116768280	116768370	NM_000492	0	+
+chr7	116769252	116769416	NM_000492	0	+
+chr7	116770552	116770678	NM_000492	0	+
+chr7	116774104	116774351	NM_000492	0	+
+chr7	116776020	116776113	NM_000492	0	+
+chr7	116782645	116782828	NM_000492	0	+
+chr7	116793468	116793660	NM_000492	0	+
+chr7	116821743	116821838	NM_000492	0	+
+chr7	116824357	116824444	NM_000492	0	+
+chr7	116825938	116826662	NM_000492	0	+
+chr7	116828934	116829063	NM_000492	0	+
+chr7	116836830	116836868	NM_000492	0	+
+chr7	116837536	116837787	NM_000492	0	+
+chr7	116840678	116840758	NM_000492	0	+
+chr7	116844523	116844674	NM_000492	0	+
+chr7	116845585	116845813	NM_000492	0	+
+chr7	116848617	116848718	NM_000492	0	+
+chr7	116861526	116861775	NM_000492	0	+
+chr7	116876442	116876598	NM_000492	0	+
+chr7	116886846	116886936	NM_000492	0	+
+chr7	116898692	116898865	NM_000492	0	+
+chr7	116899463	116899569	NM_000492	0	+
+chr7	116900912	116902666	NM_000492	0	+
+chr7	116944658	116945787	AF377960	0	-
+chr7	116952022	116952124	AF377960	0	-
+chr7	116953508	116953641	AF377960	0	-
+chr7	116955071	116955135	AF377960	0	-
+chr7	116958551	116958737	AF377960	0	-
+chr7	116959056	116959262	AF377960	0	-
+chr7	116962093	116962272	AF377960	0	-
+chr7	116968917	116969105	AF377960	0	-
+chr7	116969273	116969426	AF377960	0	-
+chr7	116979835	116979935	AF377960	0	-
+chr7	116980017	116980104	AF377960	0	-
+chr7	116990559	116990639	AF377960	0	-
+chr7	116991879	116991975	AF377960	0	-
+chr7	116994439	116994715	AF377960	0	-
+chr7	117001063	117001181	AF377960	0	-
+chr7	117011515	117011770	AF377960	0	-
+chr7	117014445	117014596	AF377960	0	-
+chr7	117016866	117016966	AF377960	0	-
+chr7	117018255	117018459	AF377960	0	-
+chr7	117025132	117026786	AF377960	0	-
+chr7	117044769	117044994	AF377960	0	-
+chr7	117095213	117095321	AF377960	0	-
+chr7	117107339	117107512	AF377960	0	-
+chr8	118880786	118881317	NM_000127	0	-
+chr8	118886141	118886313	NM_000127	0	-
+chr8	118888636	118888797	NM_000127	0	-
+chr8	118894291	118894381	NM_000127	0	-
+chr8	118899854	118899950	NM_000127	0	-
+chr8	118901095	118901214	NM_000127	0	-
+chr8	118903884	118904017	NM_000127	0	-
+chr8	118911649	118911769	NM_000127	0	-
+chr8	118916863	118916971	NM_000127	0	-
+chr8	118918527	118918621	NM_000127	0	-
+chr8	119191504	119193239	NM_000127	0	-
+chr9	128763240	128763501	NM_174933	0	+
+chr9	128763762	128763880	NM_174933	0	+
+chr9	128764115	128764189	NM_174933	0	+
+chr9	128768870	128769029	NM_174933	0	+
+chr9	128775614	128775690	NM_174933	0	+
+chr9	128775843	128775891	NM_174933	0	+
+chr9	128778280	128778336	NM_174933	0	+
+chr9	128778415	128778478	NM_174933	0	+
+chr9	128782201	128782330	NM_174933	0	+
+chr9	128782431	128782548	NM_174933	0	+
+chr9	128783277	128783404	NM_174933	0	+
+chr9	128783500	128783870	NM_174933	0	+
+chr9	128787362	128789566	NM_014908	0	-
+chr9	128789530	128789584	NM_015354	0	+
+chr9	128791021	128791076	NM_015354	0	+
+chr9	128794605	128794679	NM_015354	0	+
+chr9	128798182	128798267	NM_015354	0	+
+chr9	128798784	128798865	NM_015354	0	+
+chr9	128799842	128799887	NM_015354	0	+
+chr9	128800634	128800727	NM_015354	0	+
+chr9	128800847	128800967	NM_015354	0	+
+chr9	128810338	128810550	NM_015354	0	+
+chr9	128811232	128811347	NM_015354	0	+
+chr9	128812590	128812791	NM_015354	0	+
+chr9	128814992	128815082	NM_015354	0	+
+chr9	128821094	128821160	NM_015354	0	+
+chr9	128822438	128822558	NM_015354	0	+
+chr9	128823096	128823223	NM_015354	0	+
+chr9	128824381	128824534	NM_015354	0	+
+chr9	128824734	128824861	NM_015354	0	+
+chr9	128825125	128825213	NM_015354	0	+
+chr9	128825306	128825383	NM_015354	0	+
+chr9	128826732	128826847	NM_015354	0	+
+chr9	128828390	128828511	NM_015354	0	+
+chr9	128828641	128828708	NM_015354	0	+
+chr9	128829421	128829550	NM_015354	0	+
+chr9	128829879	128830019	NM_015354	0	+
+chr9	128831952	128832059	NM_015354	0	+
+chr9	128835029	128835236	NM_015354	0	+
+chr9	128835357	128835527	NM_015354	0	+
+chr9	128836205	128836275	NM_015354	0	+
+chr9	128836688	128836756	NM_015354	0	+
+chr9	128837151	128837347	NM_015354	0	+
+chr9	128839983	128840061	NM_015354	0	+
+chr9	128840370	128840456	NM_015354	0	+
+chr9	128841004	128841150	NM_015354	0	+
+chr9	128841456	128841638	NM_015354	0	+
+chr9	128843361	128843562	NM_015354	0	+
+chr9	128843716	128843809	NM_015354	0	+
+chr9	128844649	128844808	NM_015354	0	+
+chr9	128845149	128845287	NM_015354	0	+
+chr9	128846979	128847054	NM_015354	0	+
+chr9	128847135	128847363	NM_015354	0	+
+chr9	128847477	128847609	NM_015354	0	+
+chr9	128847882	128847956	NM_015354	0	+
+chr9	128848071	128848201	NM_015354	0	+
+chr9	128848334	128848928	NM_015354	0	+
+chr9	128849867	128850624	NM_020145	0	-
+chr9	128850938	128851179	NM_020145	0	-
+chr9	128851603	128851704	NM_020145	0	-
+chr9	128851952	128852042	NM_020145	0	-
+chr9	128852502	128852526	NM_020145	0	-
+chr9	128854068	128854131	NM_020145	0	-
+chr9	128856243	128856336	NM_020145	0	-
+chr9	128856603	128856737	NM_020145	0	-
+chr9	128862923	128863052	NM_020145	0	-
+chr9	128864114	128864256	NM_020145	0	-
+chr9	128869924	128870133	NM_020145	0	-