--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/cat_wrapper_out1.bed	Sat Feb 21 16:33:42 2015 +0100
@@ -0,0 +1,133 @@
+chr1	147962192	147962580	CCDS989.1_cds_0_0_chr1_147962193_r	0	-
+chr1	147984545	147984630	CCDS990.1_cds_0_0_chr1_147984546_f	0	+
+chr1	148078400	148078582	CCDS993.1_cds_0_0_chr1_148078401_r	0	-
+chr1	148185136	148185276	CCDS996.1_cds_0_0_chr1_148185137_f	0	+
+chr10	55251623	55253124	CCDS7248.1_cds_0_0_chr10_55251624_r	0	-
+chr11	116124407	116124501	CCDS8374.1_cds_0_0_chr11_116124408_r	0	-
+chr11	116206508	116206563	CCDS8377.1_cds_0_0_chr11_116206509_f	0	+
+chr11	116211733	116212337	CCDS8378.1_cds_0_0_chr11_116211734_r	0	-
+chr11	1812377	1812407	CCDS7726.1_cds_0_0_chr11_1812378_f	0	+
+chr12	38440094	38440321	CCDS8736.1_cds_0_0_chr12_38440095_r	0	-
+chr13	112381694	112381953	CCDS9526.1_cds_0_0_chr13_112381695_f	0	+
+chr14	98710240	98712285	CCDS9949.1_cds_0_0_chr14_98710241_r	0	-
+chr15	41486872	41487060	CCDS10096.1_cds_0_0_chr15_41486873_r	0	-
+chr15	41673708	41673857	CCDS10097.1_cds_0_0_chr15_41673709_f	0	+
+chr15	41679161	41679250	CCDS10098.1_cds_0_0_chr15_41679162_r	0	-
+chr15	41826029	41826196	CCDS10101.1_cds_0_0_chr15_41826030_f	0	+
+chr16	142908	143003	CCDS10397.1_cds_0_0_chr16_142909_f	0	+
+chr16	179963	180135	CCDS10401.1_cds_0_0_chr16_179964_r	0	-
+chr16	244413	244681	CCDS10402.1_cds_0_0_chr16_244414_f	0	+
+chr16	259268	259383	CCDS10403.1_cds_0_0_chr16_259269_r	0	-
+chr18	23786114	23786321	CCDS11891.1_cds_0_0_chr18_23786115_r	0	-
+chr18	59406881	59407046	CCDS11985.1_cds_0_0_chr18_59406882_f	0	+
+chr18	59455932	59456337	CCDS11986.1_cds_0_0_chr18_59455933_r	0	-
+chr18	59600586	59600754	CCDS11988.1_cds_0_0_chr18_59600587_f	0	+
+chr19	59068595	59069564	CCDS12866.1_cds_0_0_chr19_59068596_f	0	+
+chr19	59236026	59236146	CCDS12872.1_cds_0_0_chr19_59236027_r	0	-
+chr19	59297998	59298008	CCDS12877.1_cds_0_0_chr19_59297999_f	0	+
+chr19	59302168	59302288	CCDS12878.1_cds_0_0_chr19_59302169_r	0	-
+chr2	118288583	118288668	CCDS2120.1_cds_0_0_chr2_118288584_f	0	+
+chr2	118394148	118394202	CCDS2121.1_cds_0_0_chr2_118394149_r	0	-
+chr2	220190202	220190242	CCDS2441.1_cds_0_0_chr2_220190203_f	0	+
+chr2	220229609	220230869	CCDS2443.1_cds_0_0_chr2_220229610_r	0	-
+chr20	33330413	33330423	CCDS13249.1_cds_0_0_chr20_33330414_r	0	-
+chr20	33513606	33513792	CCDS13255.1_cds_0_0_chr20_33513607_f	0	+
+chr20	33579500	33579527	CCDS13256.1_cds_0_0_chr20_33579501_r	0	-
+chr20	33593260	33593348	CCDS13257.1_cds_0_0_chr20_33593261_f	0	+
+chr21	32707032	32707192	CCDS13614.1_cds_0_0_chr21_32707033_f	0	+
+chr21	32869641	32870022	CCDS13615.1_cds_0_0_chr21_32869642_r	0	-
+chr21	33321040	33322012	CCDS13620.1_cds_0_0_chr21_33321041_f	0	+
+chr21	33744994	33745040	CCDS13625.1_cds_0_0_chr21_33744995_r	0	-
+chr22	30120223	30120265	CCDS13897.1_cds_0_0_chr22_30120224_f	0	+
+chr22	30160419	30160661	CCDS13898.1_cds_0_0_chr22_30160420_r	0	-
+chr22	30665273	30665360	CCDS13901.1_cds_0_0_chr22_30665274_f	0	+
+chr22	30939054	30939266	CCDS13903.1_cds_0_0_chr22_30939055_r	0	-
+chr5	131424298	131424460	CCDS4149.1_cds_0_0_chr5_131424299_f	0	+
+chr5	131556601	131556672	CCDS4151.1_cds_0_0_chr5_131556602_r	0	-
+chr5	131621326	131621419	CCDS4152.1_cds_0_0_chr5_131621327_f	0	+
+chr5	131847541	131847666	CCDS4155.1_cds_0_0_chr5_131847542_r	0	-
+chr6	108299600	108299744	CCDS5061.1_cds_0_0_chr6_108299601_r	0	-
+chr6	108594662	108594687	CCDS5063.1_cds_0_0_chr6_108594663_f	0	+
+chr6	108640045	108640151	CCDS5064.1_cds_0_0_chr6_108640046_r	0	-
+chr6	108722976	108723115	CCDS5067.1_cds_0_0_chr6_108722977_f	0	+
+chr7	113660517	113660685	CCDS5760.1_cds_0_0_chr7_113660518_f	0	+
+chr7	116512159	116512389	CCDS5771.1_cds_0_0_chr7_116512160_r	0	-
+chr7	116714099	116714152	CCDS5773.1_cds_0_0_chr7_116714100_f	0	+
+chr7	116945541	116945787	CCDS5774.1_cds_0_0_chr7_116945542_r	0	-
+chr8	118881131	118881317	CCDS6324.1_cds_0_0_chr8_118881132_r	0	-
+chr9	128764156	128764189	CCDS6914.1_cds_0_0_chr9_128764157_f	0	+
+chr9	128787519	128789136	CCDS6915.1_cds_0_0_chr9_128787520_r	0	-
+chr9	128882427	128882523	CCDS6917.1_cds_0_0_chr9_128882428_f	0	+
+chr9	128937229	128937445	CCDS6919.1_cds_0_0_chr9_128937230_r	0	-
+chrX	122745047	122745924	CCDS14606.1_cds_0_0_chrX_122745048_f	0	+
+chrX	152648964	152649196	CCDS14733.1_cds_0_0_chrX_152648965_r	0	-
+chrX	152691446	152691471	CCDS14735.1_cds_0_0_chrX_152691447_f	0	+
+chrX	152694029	152694263	CCDS14736.1_cds_0_0_chrX_152694030_r	0	-
+chr1	147962192	147962580	NM_005997_cds_0_0_chr1_147962193_r	0	-
+chr1	147984545	147984630	BC007833_cds_0_0_chr1_147984546_f	0	+
+chr1	148078400	148078582	AJ011123_cds_0_0_chr1_148078401_r	0	-
+chr1	148185136	148185276	NM_002796_cds_0_0_chr1_148185137_f	0	+
+chr10	55251623	55253124	AY029205_cds_0_0_chr10_55251624_r	0	-
+chr11	116124407	116124501	AK057832_cds_0_0_chr11_116124408_r	0	-
+chr11	116206508	116206563	NM_000040_cds_1_0_chr11_116206509_f	0	+
+chr11	116211733	116212337	BC005380_cds_0_0_chr11_116211734_r	0	-
+chr11	130745911	130745993	AY358331_cds_0_0_chr11_130745912_f	0	+
+chr12	38440094	38440321	NM_052885_cds_0_0_chr12_38440095_r	0	-
+chr12	38905200	38905351	AY792511_cds_0_0_chr12_38905201_f	0	+
+chr13	112381694	112381953	NM_207440_cds_1_0_chr13_112381695_f	0	+
+chr13	29680676	29680875	NM_032116_cds_0_0_chr13_29680677_r	0	-
+chr14	98521864	98521922	U88895_cds_0_0_chr14_98521865_f	0	+
+chr14	98710240	98712285	NM_022898_cds_0_0_chr14_98710241_r	0	-
+chr15	41486872	41487060	BX537418_cds_0_0_chr15_41486873_r	0	-
+chr15	41673708	41673857	AK223365_cds_0_0_chr15_41673709_f	0	+
+chr15	41679161	41679250	NM_153700_cds_0_0_chr15_41679162_r	0	-
+chr15	41773540	41773689	AK223365_cds_0_0_chr15_41773541_f	0	+
+chr16	142908	143003	NM_005332_cds_0_0_chr16_142909_f	0	+
+chr16	179197	179339	BC065198_cds_0_0_chr16_179198_r	0	-
+chr16	244413	244681	AK057165_cds_2_0_chr16_244414_f	0	+
+chr16	259268	259383	AB016929_cds_0_0_chr16_259269_r	0	-
+chr18	23786114	23786321	NM_001792_cds_0_0_chr18_23786115_r	0	-
+chr18	59406881	59407046	NM_012397_cds_1_0_chr18_59406882_f	0	+
+chr18	59455932	59456337	AB046400_cds_0_0_chr18_59455933_r	0	-
+chr18	59528407	59528575	AY792326_cds_0_0_chr18_59528408_f	0	+
+chr19	59068595	59069564	BC013995_cds_1_0_chr19_59068596_f	0	+
+chr19	59236026	59236146	NM_198481_cds_0_0_chr19_59236027_r	0	-
+chr19	59297998	59298008	NM_004542_cds_0_0_chr19_59297999_f	0	+
+chr19	59318205	59318718	AK128544_cds_3_0_chr19_59318206_r	0	-
+chr2	118288583	118288668	NM_006773_cds_0_0_chr2_118288584_f	0	+
+chr2	118390395	118390500	BC005078_cds_0_0_chr2_118390396_r	0	-
+chr2	220108689	220109267	AY125465_cds_0_0_chr2_220108690_f	0	+
+chr2	220229609	220230869	NM_024536_cds_0_0_chr2_220229610_r	0	-
+chr20	33330413	33330423	NM_181466_cds_0_0_chr20_33330414_r	0	-
+chr20	33485370	33486123	BC085019_cds_1_0_chr20_33485371_f	0	+
+chr20	33488491	33489122	NM_000557_cds_1_0_chr20_33488492_r	0	-
+chr20	33513606	33513792	AF022655_cds_1_0_chr20_33513607_f	0	+
+chr21	32687402	32687588	NM_032910_cds_0_0_chr21_32687403_f	0	+
+chr21	32869641	32870022	NM_018277_cds_3_0_chr21_32869642_r	0	-
+chr21	33321040	33322012	NM_005806_cds_1_0_chr21_33321041_f	0	+
+chr21	33728358	33728724	AK129657_cds_0_0_chr21_33728359_r	0	-
+chr22	30120223	30120265	NM_004147_cds_0_0_chr22_30120224_f	0	+
+chr22	30160419	30160661	BC032941_cds_0_0_chr22_30160420_r	0	-
+chr22	30228824	30228916	NM_001007467_cds_1_0_chr22_30228825_f	0	+
+chr22	30340151	30340376	CR456540_cds_0_0_chr22_30340152_r	0	-
+chr5	131311206	131311254	AF099740_cds_11_0_chr5_131311207_r	0	-
+chr5	131424298	131424460	NM_000588_cds_0_0_chr5_131424299_f	0	+
+chr5	131556601	131556672	BC035813_cds_0_0_chr5_131556602_r	0	-
+chr5	131621326	131621419	BC003096_cds_0_0_chr5_131621327_f	0	+
+chr6	108299600	108299744	NM_007214_cds_0_0_chr6_108299601_r	0	-
+chr6	108594662	108594687	NM_003269_cds_0_0_chr6_108594663_f	0	+
+chr6	108640045	108640151	NM_003795_cds_0_0_chr6_108640046_r	0	-
+chr6	108722976	108723115	NM_145315_cds_0_0_chr6_108722977_f	0	+
+chr7	113660517	113660685	AF467257_cds_1_0_chr7_113660518_f	0	+
+chr7	116512159	116512389	NM_003391_cds_0_0_chr7_116512160_r	0	-
+chr7	116714099	116714152	NM_000492_cds_0_0_chr7_116714100_f	0	+
+chr7	116945541	116945787	AF377960_cds_0_0_chr7_116945542_r	0	-
+chr8	118881131	118881317	NM_000127_cds_0_0_chr8_118881132_r	0	-
+chr9	128764156	128764189	BC051300_cds_0_0_chr9_128764157_f	0	+
+chr9	128787519	128789136	NM_014908_cds_0_0_chr9_128787520_r	0	-
+chr9	128789552	128789584	NM_015354_cds_0_0_chr9_128789553_f	0	+
+chr9	128850516	128850624	AB058751_cds_0_0_chr9_128850517_r	0	-
+chrX	122745047	122745924	NM_001167_cds_1_0_chrX_122745048_f	0	+
+chrX	152648964	152649196	NM_000425_cds_0_0_chrX_152648965_r	0	-
+chrX	152691446	152691471	AF101728_cds_0_0_chrX_152691447_f	0	+
+chrX	152694029	152694263	BC052303_cds_0_0_chrX_152694030_r	0	-