--- a/test-data/fastq_dir/reads-sample-small.fastq-siRNAs-transcripts_uni.fastq	Thu Jan 17 09:56:52 2019 -0500
+++ b/test-data/fastq_dir/reads-sample-small.fastq-siRNAs-transcripts_uni.fastq	Thu Jan 24 13:09:46 2019 -0500
@@ -1,83 +1,15 @@
-@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
 +
@@ -86,231 +18,27 @@
 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