--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastq_dir/reads-sample-small.fastq-siRNAs-transcripts_uni.fastq	Wed Jan 16 08:18:13 2019 -0500
@@ -0,0 +1,316 @@
+@HWI-ST132:678:C1LFKACXX:6:1215:7425:70721
+TTTAAAAATTCGCGCCCTGAC
++
+GGGBGIIHADHHHFDDFFCC@
+@HWI-ST132:678:C1LFKACXX:6:1107:4740:59863
+CATGTCGTGGCTATACAGGCA
++
+@CCFFFFDDFFHHJJJJJGIJ
+@HWI-ST132:678:C1LFKACXX:6:1110:13407:81154
+TATACAGGCAGTAGAGCAGGG
++
+@CCFFFFFGHHHHGIHIJHII
+@HWI-ST132:678:C1LFKACXX:6:1208:19446:35829
+TATACAGGCAGTAGAGCAGGG
++
+BCCDDFDFHHHFFHGEFFGIJ
+@HWI-ST132:678:C1LFKACXX:6:1311:4516:46469
+TATACAGGCAGTAGAGCAGGG
++
+@@@DFDFF@FHBHIGGGBBGH
+@HWI-ST132:678:C1LFKACXX:6:2102:18209:60973
+GTAGTGTCCTCGGCCCCCTGC
++
+IGJJJIHGF@HHFFFFDDBCB
+@HWI-ST132:678:C1LFKACXX:6:2107:16133:23528
+CAAGGTAGTGTCCTCGGCCCC
++
+JJIJJIJJHHFFFFFEFFCC@
+@HWI-ST132:678:C1LFKACXX:6:1105:9134:90339
+CCACAAGGTAGTGTCCTCGGC
++
+3<JJJJJHHFFDADDB?FB@@
+@HWI-ST132:678:C1LFKACXX:6:1214:4589:21667
+CCACAAGGTAGTGTCCTCGGC
++
+IGIIHEHGHFFFAFFFFFC@B
+@HWI-ST132:678:C1LFKACXX:6:1113:8038:50061
+ATTGTAAGGATTATGGAAGCC
++
+JIIJJJJJHHHHHEDDDDBBB
+@HWI-ST132:678:C1LFKACXX:6:1313:3092:45831
+ATTGTAAGGATTATGGAAGCC
++
+JGJHGGGEBFHFHDFDDFC@@
+@HWI-ST132:678:C1LFKACXX:6:1315:9832:44147
+ATTGTAAGGATTATGGAAGCC
++
+IFIGF>E<3FDADDB==A?=1
+@HWI-ST132:678:C1LFKACXX:6:2107:18504:90825
+ATTGTAAGGATTATGGAAGCC
++
+HFFA>2<JHHHFFFFFDFBBB
+@HWI-ST132:678:C1LFKACXX:6:1305:2494:20888
+CTTCGTTGTCGGCTTAAGACT
++
+HF9IHDGBHFCFFFEDFFC@@
+@HWI-ST132:678:C1LFKACXX:6:1308:7696:86834
+CTTCGTTGTCGGCTTAAGACT
++
+HJJIIIIHF@DHHFDBFFB@@
+@HWI-ST132:678:C1LFKACXX:6:2103:15073:18548
+CTTCGTTGTCGGCTTAAGACT
++
+JIGGEA<20@0A32224B=14
+@HWI-ST132:678:C1LFKACXX:6:2105:19555:27066
+CTTCGTTGTCGGCTTAAGACT
++
+JJIJJIJIHAHHHFFDFFBCB
+@HWI-ST132:678:C1LFKACXX:6:2108:8901:73378
+CTTCGTTGTCGGCTTAAGACT
++
+JJJJJJJJHGHHHFFFFFCBB
+@HWI-ST132:678:C1LFKACXX:6:1313:16120:41247
+TCTTCGTTGTCGGCTTAAGAC
++
+F??DE@A@1FFFFDDDDD?8@
+@HWI-ST132:678:C1LFKACXX:6:1314:16626:18588
+TCTTCGTTGTCGGCTTAAGAC
++
+C9FIHHGGAFHHFDBADD@@?
+@HWI-ST132:678:C1LFKACXX:6:2108:9483:4135
+TCTTCGTTGTCGGCTTAAGAC
++
+HF9JJJJIHHHHHFFFFFBCB
+@HWI-ST132:678:C1LFKACXX:6:1110:13753:56378
+TTTCTTCGTTGTCGGCTTAAG
++
+IIGHE@1IHHHHDFDEFF@@@
+@HWI-ST132:678:C1LFKACXX:6:2108:8693:52625
+TTTCTTCGTTGTCGGCTTAAG
++
+HGIIHIHGHHHHHFFFFFBCB
+@HWI-ST132:678:C1LFKACXX:6:1102:14940:58653
+TTATTTCTTCGTTGTCGGCTT
++
+JJJJIHGHDCFHHFFFFFCCB
+@HWI-ST132:678:C1LFKACXX:6:1205:17717:14363
+TTATTTCTTCGTTGTCGGCTT
++
+JJJJHGCFHHHHHFFFFFCCC
+@HWI-ST132:678:C1LFKACXX:6:1209:4476:91514
+TTATTTCTTCGTTGTCGGCTT
++
+JIJJJIJJHHHHHFFFFFCCC
+@HWI-ST132:678:C1LFKACXX:6:2105:20298:47029
+TTATTTCTTCGTTGTCGGCTT
++
+JJJJIGFAHGHHHFFFFFCCC
+@HWI-ST132:678:C1LFKACXX:6:1108:9462:85509
+TTTATTTCTTCGTTGTCGGCT
++
+IGFIIFIJHGHHHEFFFFCC@
+@HWI-ST132:678:C1LFKACXX:6:1110:11726:92535
+TTTATTTCTTCGTTGTCGGCT
++
+JIGIHG@IHGHHHFFFFFCCC
+@HWI-ST132:678:C1LFKACXX:6:1115:13091:61553
+TTTATTTCTTCGTTGTCGGCT
++
+FFE:FECA?DFFFDDB4+=@?
+@HWI-ST132:678:C1LFKACXX:6:1205:13792:13310
+TTTATTTCTTCGTTGTCGGCT
++
+GGHGHGHFAFHHHFFFFFCC@
+@HWI-ST132:678:C1LFKACXX:6:1206:8454:66983
+TTTATTTCTTCGTTGTCGGCT
++
+JJIHGC:IHBHHHFFFFFCCC
+@HWI-ST132:678:C1LFKACXX:6:1207:14397:31782
+TTTATTTCTTCGTTGTCGGCT
++
+IG@IHGHIHGHHHFFFFFCCC
+@HWI-ST132:678:C1LFKACXX:6:1212:12155:21211
+TTTATTTCTTCGTTGTCGGCT
++
+HGFHHEHHFHHHHFFFFDCCB
+@HWI-ST132:678:C1LFKACXX:6:1215:9718:26126
+TTTATTTCTTCGTTGTCGGCT
++
+EHAD@HGGDDDHHDDFFD@@@
+@HWI-ST132:678:C1LFKACXX:6:1303:16630:18638
+TTTATTTCTTCGTTGTCGGCT
++
+HHJJJHIIFHHHHFFFFFCCC
+@HWI-ST132:678:C1LFKACXX:6:1305:4465:39807
+TTTATTTCTTCGTTGTCGGCT
++
+GC)JIJJJHHHHHFFFFFCCC
+@HWI-ST132:678:C1LFKACXX:6:1305:18383:99803
+TTTATTTCTTCGTTGTCGGCT
++
+JJIGC>2>3AHHHFFFFFCCC
+@HWI-ST132:678:C1LFKACXX:6:2102:14700:71462
+TTTATTTCTTCGTTGTCGGCT
++
+FGGHE<+IHHHHHFFFFFBCB
+@HWI-ST132:678:C1LFKACXX:6:2105:13617:68367
+TTTATTTCTTCGTTGTCGGCT
++
+GC1HE<+IHHHHHDDDDD@@@
+@HWI-ST132:678:C1LFKACXX:6:2105:19074:82706
+TTTATTTCTTCGTTGTCGGCT
++
+HE1IIIIGF?HHHDDDDD@@@
+@HWI-ST132:678:C1LFKACXX:6:2105:12588:90115
+TTTATTTCTTCGTTGTCGGCT
++
+JJJJJHJIHFHHHFFFFFCCC
+@HWI-ST132:678:C1LFKACXX:6:2107:6251:60107
+TTTATTTCTTCGTTGTCGGCT
++
+HB@JJHJIHHHHHFFFFFCCC
+@HWI-ST132:678:C1LFKACXX:6:2109:11439:45695
+TTTATTTCTTCGTTGTCGGCT
++
+JJJIHGHIFHHHHFFFFFCCC
+@HWI-ST132:678:C1LFKACXX:6:1211:17814:64440
+CTTTATTTCTTCGTTGTCGGC
++
+IIIIIIIHHHHHHFDB=4?@@
+@HWI-ST132:678:C1LFKACXX:6:1307:19394:48868
+CTTTATTTCTTCGTTGTCGGC
++
+GF<IHHIJHHHHHFFDDF@@@
+@HWI-ST132:678:C1LFKACXX:6:1316:17264:85131
+CTTTATTTCTTCGTTGTCGGC
++
+IIIIIIIIHHHHHFDD=4?::
+@HWI-ST132:678:C1LFKACXX:6:1115:13122:92533
+GATCTTTATTTCTTCGTTGTC
++
+JIIJJJJJHHGHHAFFFD@@;
+@HWI-ST132:678:C1LFKACXX:6:1116:15851:89973
+GATCTTTATTTCTTCGTTGTC
++
+HFGHFEGGHDHFDFFFFFC@@
+@HWI-ST132:678:C1LFKACXX:6:1303:3205:5702
+CTTTTATTTATTGAATCTTCT
++
+BCCFFFFFHHHHHHEHIJJJJ
+@HWI-ST132:678:C1LFKACXX:6:1311:7780:75331
+TATTATTTTTCCAACTGTTCT
++
+@@@FFFEAHHDHHHBGH<IHH
+@HWI-ST132:678:C1LFKACXX:6:1312:5511:15085
+TATTATTTTTCCAACTGTTCT
++
+@CCFFFFFHHHHH@GIJIIJJ
+@HWI-ST132:678:C1LFKACXX:6:2107:17724:13368
+ATTGAGAGTCGGCGTTCGTCA
++
+B@BFFFDFFHH:DHIJJJJJJ
+@HWI-ST132:678:C1LFKACXX:6:1307:8604:58747
+TTGAGAGTCGGCGTTCGTCAT
++
+BBCFDDFDFHFHHGIJJFHIJ
+@HWI-ST132:678:C1LFKACXX:6:1215:11848:43824
+TGAGAGTCGGCGTTCGTCATG
++
+CCCFFFFFHHHHFHJHGHGII
+@HWI-ST132:678:C1LFKACXX:6:2109:18960:100005
+TGAGAGTCGGCGTTCGTCATG
++
+=BBF:=2AFCF@0BE?FGHJJ
+@HWI-ST132:678:C1LFKACXX:6:1209:18683:51205
+GTCGGCGTTCGTCATGCTCGC
++
+BBBFFFFFHFHFHHHHIIJJJ
+@HWI-ST132:678:C1LFKACXX:6:1213:4432:47194
+GTCGGCGTTCGTCATGCTCGC
++
+@??DDD:DHHDACEAGIEH;G
+@HWI-ST132:678:C1LFKACXX:6:1309:20184:93600
+GTCGGCGTTCGTCATGCTCGC
++
+@@@D?DDDHHHBAH;FFGGG<
+@HWI-ST132:678:C1LFKACXX:6:1314:14515:11013
+AGCGCGAGCATGACGAACGCC
++
+JIJIGIHGHDHHGFFFFF@B@
+@HWI-ST132:678:C1LFKACXX:6:1310:19583:64029
+CAGCGCGAGCATGACGAACGC
++
+JJIHHECBHGHHHFFFFFCCC
+@HWI-ST132:678:C1LFKACXX:6:2108:10695:38989
+ACCGATTTTGTGCGGAGCACG
++
+@CCFFFFFHHFHHCF@EGIGJ
+@HWI-ST132:678:C1LFKACXX:6:1209:11040:19674
+TCTTCACACGTCGGCGATCGA
++
+@@@DDFFFFHFFDHJGIDD@G
+@HWI-ST132:678:C1LFKACXX:6:1116:11668:16725
+TAAGAATTCCGAAACGCCATC
++
+IHEGAG@ED8FDDBBDDD=+?
+@HWI-ST132:678:C1LFKACXX:6:1208:13565:65937
+CGATGTGTTTGTTCGCCCGTC
++
+@@CFFBDBFHHDFHAFHI)@F
+@HWI-ST132:678:C1LFKACXX:6:1209:11809:98806
+AACCTCCTAGTCGCTGTGACT
++
+JJIJIJIGGHHHHFFFFFBCB
+@HWI-ST132:678:C1LFKACXX:6:1206:18658:28841
+CAGGTTAACCTCCTAGTCGCT
++
+JIJJJJJJHHHHHFFFDFCCB
+@HWI-ST132:678:C1LFKACXX:6:1309:8277:38084
+CAGGTTAACCTCCTAGTCGCT
++
+IIIJIJJIHHHHHFFFDFC@@
+@HWI-ST132:678:C1LFKACXX:6:2103:17347:32864
+TTCTTGAACTTGCGAGCACCG
++
+CCCFFFFFHHHAAFC3BEHIJ
+@HWI-ST132:678:C1LFKACXX:6:2107:8602:93094
+TTCTTGAACTTGCGAGCACCG
++
+CCCFFFFFHHHDHCCFFHIJJ
+@HWI-ST132:678:C1LFKACXX:6:2106:14321:83705
+TTGCATTAATCTGAAAGTTGC
++
+IHIGIJJJHHHHHFFFFFCCC
+@HWI-ST132:678:C1LFKACXX:6:1306:11622:66870
+CAAATTGGCTTTCCGTCGACT
++
+@@@DFFFFHHGHFHJJEIGHH
+@HWI-ST132:678:C1LFKACXX:6:1107:16523:27164
+CCAAGGAGTCGGCAGCTGAAG
++
+@@@DDDDDCD?FF1)AEGGII
+@HWI-ST132:678:C1LFKACXX:6:1206:20690:60805
+AGTGGGGCCAGAGGGGCTGCT
++
+>?:C?:@BFFFCHDADDD@?<
+@HWI-ST132:678:C1LFKACXX:6:1309:15210:100042
+CGGCTTTGTCACTGTTTGATC
++
+@CBFFFFFHHHHHIGHHIGJJ
+@HWI-ST132:678:C1LFKACXX:6:2108:11541:97204
+TATTGAACTGAAGCCCCCGGC
++
+CCCFFFFFHHHHGJJJJJ@GG
+@HWI-ST132:678:C1LFKACXX:6:2102:9712:32185
+ATTGAACTGAAGCCCCCGGCC
++
+?@@BBDBDDFFADHIIIH)?F
+@HWI-ST132:678:C1LFKACXX:6:1313:12783:74925
+GAGCGGGTTTGGCCGGGGGCT
++
+JJJJJJJJHGHHHDFFFFCCB
+@HWI-ST132:678:C1LFKACXX:6:2103:17748:30120
+TGCACGATTCCAATAGTGCTG
++
+IJIGCJIJHHHHHFFFFFCCC