diff --git a/data/test_PE1_2.fq b/data/test_PE1_2.fq
new file mode 100644
index 0000000000000000000000000000000000000000..17ccf78a57985bc6c9816eedf04c298ca639563e
--- /dev/null
+++ b/data/test_PE1_2.fq
@@ -0,0 +1,160 @@
+@NS500443:42:H3MH2AFXX:4:21612:18494:19326/1
+GGTTCTGTTGGCTCAAACGCCGTCACTTCATTGATCAAAAGCTTATAATGCGTGCCAAAGTCCGCCATCGAGACGACTACGCCTTCCCCTGCTTTCCCGTCAAAAACGAGTCTTGCCGGATCTTCACGGTCTCCCCTCGAAAGCGGCGAAA
++
+6A/AAEEEEAEE6EEEAEEEE/EEAE/EE/EEA/EEEEE6AEAEAEAEEEEE/EEEEEE/EEEEEEEAEE/EEE//AEEEEEEEEAEEA/EAE/EA<<6/AEEA//A//AEEEA6AA<EE/AEEE/A///AEEE//EEEEEEEEAAEAAEA
+@NS500443:42:H3MH2AFXX:4:21612:18284:19327/1
+GCGTTTACCCATTCTTCCTATGTCAATGAACATCGTAAAGAACATTTAAAAGACAATGAAAGATTAGAATTTCTAGGAGATGCGGTATTAGAGTTAACTGTATCTGATTATTTATTTAAAAAGTATCCGGACATGGCGGAAGGTCAAATGA
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEAEEEEEAEEEEEEEAEEEEEEEEEEEAE<EEEAEAAEEEAEAEEAEE/
+@NS500443:42:H3MH2AFXX:4:21612:12448:19327/1
+CACGATGGGTGCCTTTTTGCATGTGAATACGGACAAATTAGATGTGCGGCGCTATCTTGAGATGGTGGAGTCGAGCAGTCCGTCTTATATGGTGATGGCTTCGCTTGATGTGGCGCGGCGCTATGTGGCGCTTTATTCGGATGAGGATTTT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEE/EEEEEEEAEEEEEEEEEEEE
+@NS500443:42:H3MH2AFXX:4:21612:3226:19328/1
+CTTGAAGCGTCATGATAAGGTGTTTTCGGAAATAGATGAATATATTGCGGACTTGCGGAAAAATAACGCCAAGCTTGCGGATTTGATGCAAGAAATTTGGGACGAGATTCAGGAAAATCCAGAAGCGTATCGTGATAAAAATGTATCGA
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEAEEEEEA<EEEEEEAEEEEEEEEEEE<
+@NS500443:42:H3MH2AFXX:4:21612:21221:19328/1
+GTGTTAACCAAATTCGTGCACAAATGGAAGAAACTACTTCTGATTTCGATAAAGAAAAATTACAAGAACGTTTGGCAAAACTTGCTGGCGGCGTAGCTGTCATTAAAGTAGGTGCTGCAACTGAAACAGAACTAAAAGAACGTAAACTTCG
++
+AAAAAEAEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEE<EAEEEEEEEEEEEEEEEEEEEEEEAEAEE/EEE
+@NS500443:42:H3MH2AFXX:4:21612:11696:19332/1
+ATGTGATACACCGGAGAATATACTAAAAAATCCTGAAACTGATTTTGTTCGTAATTTTCTTGAGTCTGGCAATCTTTTACCAAAAACATTATTTGACCGTTCAATCAAGATTTCTGATTTAGTCACTAAAAATTTCTGTACTCAGGCACAA
++
+AAAAAEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEEEEEEEEE<AEEEEEAEEEEEEEEEEEEEEEE
+@NS500443:42:H3MH2AFXX:4:21612:8548:19332/1
+TAACATGGAAGCTTACTATCAGGAAGCGGGAAGAGCTGGCCGGGATGGACTGCCAAGTGATTGTGTGCTGCTTTTTTCACCACAAGATGCACATCTACAGCATTACTTGATTGAGCAGTCAGAACTTCCTGAAGATCGTAAGGAAAACGAA
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEAEA
+@NS500443:42:H3MH2AFXX:4:21612:5092:19335/1
+ACCTACTTCTTGCAACATTTCCATGTCATTTAGACCATCGCCGAATGCATAAGTATCTTCCATTGAAAAGCCTAATTTCTTGATCATATTACGAATTCCGCGAGCTTTAGAGCCATCACTTGGACAAACATCAACAGAAACATCATGCCAG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEAEEEEEE/EEEEEEAAEE<EEEEA6AAEAEEEEEAEEEAEEEEEE6EEEEEAEA
+@NS500443:42:H3MH2AFXX:4:21612:3939:19336/1
+GGTGGAAAACATGAACGGAAAAAATATTCTACTTGCAGTGTCTGGCGGCATTGCAGTTTATAAAGCAGTAGCGCTAACGAGTAAACTCACGCAAGCAGGTGCCAATGTAAAAGTGATGATGACACGTCACGCACAGGAATTTGTTCCACCG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAE//EEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEAEE/AEEEEE/EEEAEEEEEEEEEEAEEEAEE/
+@NS500443:42:H3MH2AFXX:4:21612:7738:19336/1
+TTCTTTCCCAGAAAGCCCTACAAGTTGAATCAATTCTTGCACACGTTCTTTTCGTTCTGCTCGTTTCACTCCGGCAATTTCAAGCGGAAAAGCAATGTTTTCAAATACTGTTCGCGACCAGAGCAAGTTGAAGTGCTGGAAAATCATCCCG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAAE<EEEEEEEAEEEEAEEEEEEEEEEEEEEEEE<EEEEAAAEEEEEEEAEEEEEAEEEEEEEEEAEEEEEEEEEAEEEEA<
+@NS500443:42:H3MH2AFXX:4:21612:11553:19339/1
+GTGTGAATACTACCGTTTGTTTATGATAACCGATTCCTTCACCGTTTATCCCCATTCTTTTAATTTCAAGCGGAAAAGTCTGTCCCACTTTTATCTTTGCTCCGTCCAACCACATCTCCTCCGTTTCAATTCTTCATCCATACTATCAAAA
++
+AAAAAEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEAE<EEEEEEAEEEEEEEEEEEAAEEEEEEEAEEEEEEEEEEEEEEEEEEE
+@NS500443:42:H3MH2AFXX:4:21612:20775:19341/1
+GCTTTTTCATTTTTATATATTCCATTTCGCGTAAAAAGAATTTATCAATAAAAATCTTGATTTTTTCTTACAACAAAAGACGCTGGCAGATTTGAAAAATCAATCTACCAGCGTCTTTTGTTCGGCTAAAAACTATATATTAAGCATCTC
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAEEEAEEAEEEEEEEEEEEEEEEEEEEEEEEEEAEAEEEE<EEEEEEEE<EEE<EEEEEEEEEEEEEEEEAEEEEE
+@NS500443:42:H3MH2AFXX:4:21612:2150:19342/1
+GCTCTTTTTCCGCCGCGATTTCCCTCAGCTTCGCATAAAGCGGCATGTGGAAAATGGTCATAGCTTCCATAACCACAACCTTTTTTTCGCGAGAAACGCGGAGAACATCCTCGAGTTCACGGGAACTCACCGTAATCGCCTTCTCCACCAA
++
+AAAAAAEEEEAEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEA/EEAE//EEEAEAEEEEEEEEEA/EAEEEE/EAAEEEAAA<EE<EAEEEAEEEAEAE/EEEAE/<EEEE<EEEAEEEEE/
+@NS500443:42:H3MH2AFXX:4:21612:2100:19343/1
+AGATGACATTATTGGAGGAAGCGGCAACCCCAAGGTTACTAGCCTTCGTCCAACCAACTAAATTCGATCCATCTTTCATACGTTGCCAAACGACGCCATCAACAGTTACTTCACGGTCAACAGTAAGGTCTTTGCCATACACGTTCTTCAA
++
+AAAAA/EEEEEAEEEEEEEEE/AEEEAEE/AEE/AEAEE/EEAE//EEEEEEEEEAEE/EEE6EAEEE/AEAEEEEEEEEEAEE/<EEEEAE/</EE/EEEE<EE/A/AEE/<///AEE/EEEEEEE<EAEEA//AEEEA<<</E<AAEAE
+@NS500443:42:H3MH2AFXX:4:21612:11502:19343/1
+GTTTATGTAGCTTCACAAGACGAAGAAATGAACAAAAAAGCGATGGCAATTATTGAAGATATCGTTCGCGAAGCAAAAGTGGGCGAAATCTACACAGGGAAAGTTCGTCGAATCGAAAAATTTGGGGCTTTCGTTGAATTGTTTAAAGGAA
++
+AAAAAEEEEEEEEEAAEEAEEEEEAAEEEEEEEEEEEEEEEEEEE/AEEEEEEEAEEAEAEEEEEEAAEEEEEEEEEEEEEE6EEEEEEEEE<AEEEEEEEEEEE</EAEAEEEAEEEEEEEEAEEAAEEAEAEEEEE/EE/EEEEE<E/E
+@NS500443:42:H3MH2AFXX:4:21612:24968:19344/1
+CGCTTATTTGATACGGCAGCTGTTTATAATAATGAACGTGAAGTTGGCGAAGCGATTCGCGCGGGAGGGGTTTTGCGAGAGGAACTTTTCATCAGTTCAAAAATTTGGAACGGTGACCAGGGCTACGATGAAACACTATTTGCCTTTGAGA
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEE/EEEEEEEEEEEEEEEEEEE6AEEEEAAEEEE</AEEEEEE/AEEEEEE/A6<EEEEEE<AEEAEEEE/
+@NS500443:42:H3MH2AFXX:4:21612:6916:19344/1
+GTTTCCGAACGACTTGCTAAAGAATACGGGCTTAAAACGATTTCTGATCTGCGCCCAGTGGAGCAACAAGTAAAAGTGGGCTTTACGGCAGAATTTGCTGACCGTGGTGATGGCTATAAGGGGCTAAAAGAAAAATATGGAATCACCTTTG
++
+AAAAAEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEAEEEEEEEEEEEEEEEEEEAEEEEEEEE//EEEEEEA/EEEEEEAEAEEAEEEEEAEEEEEEEEEEEEEEEE6EEEEEE</<EEEEA
+@NS500443:42:H3MH2AFXX:4:21612:15429:19346/1
+AGCTTATACAAGCCGCGTTACTTGAGAAGTAAACATCTACAATATTCCCTTTAATCGCACCACCAGTATCCCCAGCGATGGCTTCACCATATCCAGAAACGTGAACGCGCGAGCCAAGTGGAATAACACTTGGATCTACGGCAACTACTTT
++
+AAAAAEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEAEEEEEEEEEEEEEEAE<EEAEAAEEEEEEEEEEAEEEEEEEEEEA/EEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEE<EEAEAEEEEEEEE
+@NS500443:42:H3MH2AFXX:4:21612:1024:19346/1
+TCCTTCCGAAGCGTCTTCGCANTAGTCAAATTCCCATTATGNGCAAGAGCAAGTGAAGAATCTTGAAAATGAAACAAAAACGGTTGAACATTTCCAAGGCTTTTTCCGCCAGCTGTTGCATAGCGCACGTGACCAATTGCGCCACTTC
++
+AAAAAEEEAEEEEEEEEEEAE#EEEEEEEEEAEEEEAEEEE#E/EEEEEEEEEEEEE6EEEEEEEEE6EEAEEEAEEEEEE/E/EE/E/EEEE<EEAEEAEAEEEEAEAA<EEEE<EAE/EEEAEE//EEEEEEEEE/E6EEE/E/EE
+@NS500443:42:H3MH2AFXX:4:21612:4182:19348/1
+GCATGGCAATGAAGTTAAATAACGCTTCCGGCAAATAGCCTAAGTCGCGATACTGCTCGATAAATTGGATAATCGAACCATCACGCTTACTTAATTTACGGCGACTTTCATTGACAATCAACGTCATATGACCAAAAGTTGGCGGTTCCCA
++
+A6AAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEEEEEEEEAEEEEEEAEEEEEE<E<AEEEEEEEEEAEEEEEAEE<A/EEAEEEEEEEEEE<EEEEE/EEAAEAAEEEEEEE6<EAAE</</A
+@NS500443:42:H3MH2AFXX:4:21612:26730:19348/1
+ATCTCAACGGGGGGAACAGGAATTTCGAAACGGGATGTAACTTTTGAAGCCCTATTCCAACAAAAACACCAGGAGATTCCAGGGTTTGGGGAGTTGTTTCGAATGAACAGCTATCAAGAAATCGGATCAAAGGCAATGGCATCCCGCGCTA
++
+/AAAAEAE/E/EE6E6AAEEE//E6EA//A//6EEEAEEA6/EE/6E66<EE/AE/EE/EEEE////A/EEEEE/E//EE/A//EEEA//AAEEE////E/EEEA//E//6/EA6AE////A/A/AEAEEE/EAAE/<//EE</<<//AE/
+@NS500443:42:H3MH2AFXX:4:21612:25889:19349/1
+GAGCGAATCAAGTGCCTTGGAAAGAGCGGATTGCATATGCAATGAGTGACTTTGGCTGTAATACAGTTTTTCAAATTTTAGGAACGTATTTTCTTGTATTCTGTACGGATACACTTGGCGTTGCGGCAGCAGCGACTGCTGGACTTTTCG
++
+AAAAAE/EEEEEEEEEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEAEAEAEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEE/EEEEEEAEEEAEEE/AEEEAA<EEE6E6EEEEEEEEEEAA/<EE</EEEE<6
+@NS500443:42:H3MH2AFXX:4:21612:6539:19353/1
+GATGCAGTTGTTTCTAAACGGGGCTCCTGTTCAACCCGTTTTAGACCGCTTAAAATCTATTTTTGGCATTCAATCTTTTAGTCCGGTTATCAAAACAGCATTGGATGTTGAAGAAGTGAAAGAAGCTGCCTTTCAACTTGTGAATGACA
++
+A/AAAEEEEEEEEEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEE/EEEEEE/EEEEAEEEAEEEEAAEEEEAAEEEEEEEEEEEEEEE/EEE/AEEEEEEEEEEEEAEEEEEEEEEEEE/EE<E<EEEEA<AEEEAEEEEEEEEEA/EA
+@NS500443:42:H3MH2AFXX:4:21612:21998:19353/1
+TCGGTAAGCTTTCTAAATCGAGTATTGTAGAACTTTTTGTGACAACTTTGAAAGAAGAAAATTAGCAGGAGGGGAATTATGAAGCAACCTGTCGTTATTTATGTAATTTCGGATGCGATTGGAGAAACGGCTCAACATACTATTCGAGCCG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEAEE/EAEEEEAE6EEEAEEEEEEEEEEEE<EEEEAEAEEEEEEAEEEEAEEAEE/EEAEEEEEE<AEEEEA
+@NS500443:42:H3MH2AFXX:4:21612:9349:19354/1
+CCGCGATACTCCGTTCGAGTAGACACTGCGTCACGGGGCTAAGTTTCAAGCCACTTGCAACAATTTCTTCGAGTTCTGTATCGTTATGGCAAATCCCACCGCCAGACCCGCCAAGTGTATAAGCAGGGCGAACAATGACAGGATAGCCGAT
++
+AAAAAEEEAEEEEEEEEE/EEA/EEE/EAAEEEE/EAEEEAEEEEEE/E/EEEEEE6EEEEEEEEEEEEEEE/EEEEE6E<E/AE/EEEEEEEEE<EEA6/EEAEEE/A<AAEEAEE/EEEEEE/EEEA</<EE/AEE<AEAEAE<EEAA/
+@NS500443:42:H3MH2AFXX:4:21612:10100:19357/1
+CGTTGGATCCACTTCCATCATATGGGATTCCAAAATTGCTTCCTTTCCTGCCGCTAGCTCGTAGGTATAATCTTCCATAAAACCAGTATTTTCGTTATGAGCCATCACTTTCATCAACCGGTCGATCGCCGCCGTTTTCCAGTCTCCTTC
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEAEEEEEEEEEEAEAEEEEEEEEEEEEEEEAEE
+@NS500443:42:H3MH2AFXX:4:21612:5905:19357/1
+CACCTGCTACACTCGCTTCATAAAATAAATCGCAGTGGTTTTCTTGCGCCACTGCTACGAGTTCATCTCCGTGAATAGCAATTAAATCTTTATTTGCGGTTACAACACTTTTCCCTGCTTTCAGTGCATGCAAAATGTAATGATGTGCGGT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEE/EEEEEEEEEEEEEEEAEEEEEEEAEEEE
+@NS500443:42:H3MH2AFXX:4:21612:22823:19360/1
+GGATGGGCAAGCGGGAAGAGTTGGAGCGGATTAGCCAAATTGAGCCGCTTGCTGCACGTTACCGGGATGAGGTACTTGAAAAGCTTAGGAAAATGGGATGAAAAAAGAGCCGTTCGGAAGAACGGCTCTTGGCGTGTTTTGCGTTTAAAAT
++
+AA6AAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAE<EEE/EEEEAAEAEEEEA</EEEEEEA<EEEEEE
+@NS500443:42:H3MH2AFXX:4:21612:17904:19360/1
+GTAACGGTAAAAGTTATGAACGTTGGGGATGACGGTAAGATTGGTCTTTCAATCCGTAAAGCGGTTGATCGTCCGCGTCCAGAACGGAATTATGATCGGAAACCGAAGTATAACAAGAAACCAGCTGCTCAGTCCAAACAGCCGGAAGATT
++
+AAAAAEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEAEEEEEEEEEAEEEEEEEEEEAEEEAEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEA<EEEEAEEEEEAEE<EEE/EEEAEEEEA6/EEEEEEE
+@NS500443:42:H3MH2AFXX:4:21612:5361:19361/1
+CGCATTACGCGCATTCGTCTGACCCGCTTCTACCTTCTTTAATTTTAAATCTTGATTTACTTCTTCGTCTGACTCTTGTAACGTAACGCCGATGACATAAGCATATTTATTTTCAATACTTATGCCCTTATCTTGCTTTTGACTCGTTGCA
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEEEEEEEEE6<EEEEEEEE<
+@NS500443:42:H3MH2AFXX:4:21612:10976:19365/1
+TCACTAAATTTAATATCTTTTGACATAATTTAATTCCCTCCAATTTATATCGCTTTTGTTTTCTATTTTTACTTCGTAACTGCTAAAATATCACTTTCGCGAATAATTAACAGATCTTTTCCTTCATAAGTTACTTCTGTTCCAGAATATT
++
+AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEAEEEEEEEEAEEEEEEEEEEEEE6EEEEEEEEEAEAEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEA
+@NS500443:42:H3MH2AFXX:4:21612:22942:19365/1
+ATCCATGAATAAATCCACAATATCTTTTAAACGGCAGGTTTGTTTATTGATCAAAAATTCGCTATCGCCATTTCGGTAAATTCGTCTTGTCACCACTACTTCACTATAATCAAGCGGCAAGTAGCGATCATCATTGGCAAGTACGAGCGAT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEAEAAEEEEEEEA/EEEAA
+@NS500443:42:H3MH2AFXX:4:21612:14114:19366/1
+CCTTGGAAACATCACCTATGTGTTGATGTATAACCTAGGACTTGAGCTCGGGAATGCCTTTCACGCTTCTACTGAAACCGCACAAACCATTGCCTCTGTTTTTGCGCGAATCACGGGGCTCTCTATGTTCCTTGCTTATACAGGTGCATTT
++
+AAAAAEEEEEAEE6EEEEEEEEEEEEEEEAEEAEEEEEEEEEEEEEEEEEEEEEEEAEEEEE/EEEEEEEEEEEEEEEAEE6EEEEEEEEEEE/EEEEEEEEEEEEAEEEEEEEEEEEEEEEEAEEEEEEE/EE/EAEEEEEEEEEEE<E<
+@NS500443:42:H3MH2AFXX:4:21612:13612:19370/1
+GCATCTAAAATCGGATGTGAATAGTCTTCCTGTACTGTTGTTTTTAATGCATCAATTGCTGTATTTCCCGTTACAAAAACGGTCTCCGCCTTCTTATTTTCACGCAGTAAATTTTCTTTTGCCGTATCCGTTGGCGCAAAGTGCAGATCAG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEE/EEEEEEEEEEEEEEEE/EEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEA
+@NS500443:42:H3MH2AFXX:4:21612:1049:19371/1
+ATGCTTGTTATGCACTATAAATTGAAAAAGATTGACATGATCGAAGCGCTCAAATCAGTTGAGTAACAAGAGACACTCCTCTTCTAGCCAAAGAGGGGTGTTTTTTGGTTTACTTTTTGTCTAAAAAGCGATAGAATGAAAAATAGTTCAG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEE6EEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEE/EEEEEEEEEEEEEEEEE<EEEEE<EEEEEAEEEEEEEAEEEEEEEEAEEAEE<EEEEEAEE/A</A
+@NS500443:42:H3MH2AFXX:4:21612:9601:19373/1
+TCCAAAAGCTGATGGATTGCAGAAAAAGCCTCTTCACTCCCAATCATCGCTTTCATCAATAGATATTCAGAAGCATGGTAAGCTTGAAGCGTTTGTCTAACTGGCTGAGCACTTACTAAGCCACCATAAAAATCATCAGGAGGTGGCGCTA
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEAEEEEEEEAAEEEEEEEEEEEAAEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEA<EE<EEEE<EE<EEEEEEEA/EEAEEAEEEEEEAEEEEAEEEEAAEEEEE<A<A<E<<EAAEEEEEEEE
+@NS500443:42:H3MH2AFXX:4:21612:20393:19375/1
+CAGAGATTGATCGCGTACTAAACACATTGCTAGAAACGAGAAAGCCGGTTTACCTTAACTTGCCAATTGATGTTGCGGAAAGCCCCACCTCAAAACCAAGCAGGAAATTATCTGGTTCGACGGAATTAACGAGCGCAGATCAAAATTTG
++
+AAAAAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEAEEEEEAEEEEEEAEEEA/EE/EEEAAEE/EEAAA/AEE/EEE/EEEEEAE/AEE/<E/EEEAEEAEEE
+@NS500443:42:H3MH2AFXX:4:21612:18713:19376/1
+CCTTAGAAGAAATTATTTTTCCTCACTAGGAACAAAAGTATTTTTGAATTCATCCAGTGCGCTGTTCAATTTTGCTTCATCTGGAAGAGATTTTGTAGTCCGAATTTCGTCTAGTAATTCTGCATGATTATGATCAAACCACGTATTCATT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EAEEEEEAEAAEAEEEEEEEAAEEEEEEEEEEAEEA/EEEEA/A/EEEEE
+@NS500443:42:H3MH2AFXX:4:21612:16612:19377/1
+AATTGCGCCTTGAATAATAAAGCTTCGTGGAGTTTCCTTATTGTTTAATTCAGCTAAAAGAGCATTTAAAGTTTCCTTAAACTGCCACTTATCCGAATCAGCAATTTGTCCGGCATCAATTTTCATCAGCAAGTCTTCCACCAAATTTTT
++
+AAAAAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEAEEE/EEEEEEEEEEEEAEEEEA/EEE/EEEEE/EEEEEEEEEEEEE6EEEEEEEEEEEEEEEE/EEEAEEAEEE<<EEEEEEEEEE
+@NS500443:42:H3MH2AFXX:4:21612:21100:19378/1
+ATTGTGGGGTTCCTTTTTGTAGCATTGGAATGGAAATTAAAAATGGGGCTTCAGGATGCCCGCTCCATTATTTAATTCCAGAATGTAACGATGCTGTTTACCGGGGGGACTGGAAAGATGCACTTGAGCTTTTGATTAAAACAAATAACAT
++
+AAAA/EEAAE///EAEEEEAEEAAEE/EEA6AEAEEEEEEEEEE666//////AAAEE////EE<EEA/EEA/EAEEEEAE//E//E//E///E/66E<E////EE/6/AEEEEA/AA//AEEEEAAE//E//</EAE/AEEEEEEEEE//
diff --git a/data/test_PE2_2.fq b/data/test_PE2_2.fq
new file mode 100644
index 0000000000000000000000000000000000000000..c6cf6339e936d8ac8a7eca64a51c45c65ba1f812
--- /dev/null
+++ b/data/test_PE2_2.fq
@@ -0,0 +1,160 @@
+@NS500443:42:H3MH2AFXX:4:21612:18494:19326/2
+TCTTAGAGGAAGGTGGATATAATGCCGTCACATCGAACTTTGAAGATCTATACGGCATGCAGCAGCTTCCAGGTCTTGCGGTGCAACGTTTAATGGCAGATGGCTACGGTTTTGCGGGGGAAGGAGACTGGAAAACGGCGGCGATCGACCG
++
+AAA6AE/EEAAEA/EEE/EAEEAEE//EE/E/EEE/AA//EEAE//E/E6//EE6AE//E/AEAE//AE/EEE/AEE/E/E/E/EAEE/EAEE//AEEEEEEEAEEEEA/AAEAE/EA<A/A/AEEAE/EEA/A/E///</6E/EEA/AE/
+@NS500443:42:H3MH2AFXX:4:21612:18284:19327/2
+CTAAAAATTGGATGACTTTTGCAAGCCCATTATCGAGATAAAGCGCTCCGATAAAAGCTTCGAAAACATCGGCAAGCAGAGCTGGTCGATTTCTACCACCCGCTTTTTCTTCTCCTTTTCCAAGTCGAACATATTTGGAAAAATGAACG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEE/EEEAEEEEEEEEEAAAEEEEEEEEEEAEEEEEEAEE/E<EEAEEEEEEEEE
+@NS500443:42:H3MH2AFXX:4:21612:12448:19327/2
+GGATAGAATCCAGCTTGTTCCAATTGTTCAGCCAACCTATAACCCGAAAAGCCTTGTTTTCGAACAATCAATTTCAGCGGATCATCCGGACAAATCACTTCGAGTTCTTGTTTCTCCAAAAAACGTAGCCATTTCGCTCGCATTTTCCAAA
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEAEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEE<EAEAEEEEEAEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEE<EEAEEEEEEEAEEE
+@NS500443:42:H3MH2AFXX:4:21612:3226:19328/2
+TCTTGAAAGACTAGCTATATTTCTACTTCTAGAACCTTACTCTCTTCGTCGTAGCGGTAAAATTTCTTTTTCCACCACATCTTTTAAATCTAATCGAGCTGCTTTCCAGTACTTCAACTTCGGTAGAGGATTTTCTGTTTTCTTTTTATAG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEE/EEEEEEEEEE<EEEEEEEEEEEEEEEEAEEA<EEEE//AAEEEEEEEEEEEAEEEE<E<<6EEE<EEEEAEE
+@NS500443:42:H3MH2AFXX:4:21612:21221:19328/2
+GATTGGCGCTTCAAGTGAACGTAGAACAATATTTACACCTGTTTCTTCATCTCCAGTAGCTTCGATTTCTGCTACTTTCTTATAAACATTGACAAGAGCCGTTCCACCACCGGAAACAATACCTTCTTCAACAGCTGCACGTGTCGAGTTT
++
+AAAAAEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAAEE<AEEEEEEEEA/EEEAEEEAEEEEEAE/EAEEAEEEEEAEEEA
+@NS500443:42:H3MH2AFXX:4:21612:11696:19332/2
+ATTTGGATGTGCTCAATTAAAGCGGTAAGCAAATCGTCTTTTCGGTCTAGGAATGTCTCGATGAATGTATTCATGGAGTGACACCTTCTTTCAGGTTACTCGACAAGAAGGCAAGTAAATCATTCGTTGTGATAGTTGCAACTAGTAGAC
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEAEEEEEEEEEEEEEAEEEEEEEEEEEEEEEE<EAEEEEEEEEEEAEEEEEAAEE<<EEEAEEE/E
+@NS500443:42:H3MH2AFXX:4:21612:8548:19332/2
+CTTTAGCAACCATAACTTTGCCGAAGCGCTCTCCCATTCGCTTCACACAAGAAAAGACTTGCTGAGCTAGAATGGTCACATCTGTCTCAGTACCTGTATCTAAACAATTGCTGCAGTTTCCGCAATCCTCACATTCTTCCCCGAAATAGTG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEE
+@NS500443:42:H3MH2AFXX:4:21612:5092:19335/2
+TTATAACGGTCAGTATGTGATTTTTGAAGGAGAAGTCTTATTGAAAAATCCACTTCCGCAAGAATCACTTGAACGCCTAATCACTGTAGCAACAGAAAACGATCATCCTATTGTCTTCTCGGCAAGTGATACAATGCGTGTTAATTTGCCG
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEEEEAEEEEEEAEAEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEAEEAEEEEEEEEEEEEE/E/E/EEEEEEEEAEEEEEEEEEEE
+@NS500443:42:H3MH2AFXX:4:21612:3939:19336/2
+GCTACCCACACAGGGGCTTCCGTTGCAAGAATGGTTGTTGTGACCATATCGTCAGCAATGCCATTCGCCATTTTCCCAATGACATTGGCGGTAGCTGGTGCAACGATAACAAGATCCGCCCAGTCCGCTAAATCAATGTGCGCAACAACGG
++
+AAAAAEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAEEEEEEEEEE<EEEEEAEE//EE/EEEEEEEA<EEEEEEAEEEEEEAEEEAE<EEE<EEEE/EEA<EEA
+@NS500443:42:H3MH2AFXX:4:21612:7738:19336/2
+GTCGTGGGCTATTCCGGGGCAGGAAAAAGTAGTTTGATCCGAATGTTTAACGGCCTCGACCTACCAAATGCAGGCAATGTAATATTGGACAACAAAAAAAACAGACAAATTAGAGGCCGAGAACTTAGAAAAGAACGGAAAAAAAACGGGA
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEE/E6/////E///<E/EE/E///E//EEE//E//6/AA/A/E</AEEEEEE6/////EE/A/</E<A/A///A//E/A/EEEE///AE//EEEEEA/</A//
+@NS500443:42:H3MH2AFXX:4:21612:11553:19339/2
+TAGATGCTTCGATCTAAGACGTTATTTTCGTCACGCAACGCAGCTTTAATACTGCGAAAACGTGTGTTTAAAAAATAAATTTGTAAGGCAAAGGCCCAGCGAGCTGGGTCATCGTAAAACTTTTCGAGAATTCGGTTGTCCGTGATACTTT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEE6EEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEE<EEEE/AEEEEAEAEEEAEEEEE<AAEEA<AEEEEEEAA
+@NS500443:42:H3MH2AFXX:4:21612:20775:19341/2
+CATCCCCACTATCCCCCCATCCTTGTTAATTGTAAATAAGTTAACATCAAGACTACCTGAACCATTTTTTTGATGGTAAAGCACTATTCTTTGATCTTCTTGCGTCATGTTTTCCGTCAAGCTTTTTGAAGCATTTACAAAGGTGGATCGG
++
+AAAAAEEEEEEEEEEEEEAEAEAEEEEAEEEEEAEEE/EEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEE</EEAE<EA<EE<AAEE/EEEEEEEE<EEAEEEAEEEEEEEEEEEEAEEEEE/EEEEEEEEAEEEEEEEE/EE<E
+@NS500443:42:H3MH2AFXX:4:21612:2150:19342/2
+AGTATATACTTTTTGACAACGATTTCAAGAAAACATATAATAAATAACATAGAAGGCAAGAGGAAAGGGTGTCACTTATGAGTAATTTGAAATGGGCTATCGTTGGACCGGGCGGAATCGCTCACCAATTTGCAGAAGCTATGGCAAAGGA
++
+AAAAAEEEEEEEEEEAEAEEEEEEEEEEEAEAEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEE<A/<AEEAEEEEEEEAEEEEEEE/AEEAEEE/EEEEEEEEEAEEEE<E/AE/<A<EEEAE/6EEEAAEEEEEAEE/
+@NS500443:42:H3MH2AFXX:4:21612:2100:19343/2
+CCTATTTATTCTGCACCTGTCGGCTCCGCCGCTGCCACATCTGTTGGGAATTTATCGAGCTATTCCGGTAAACAAATGCGCCTCGTTCGCGAAGCAAAAGCCGGCAGTACCGTTTCTTCACAAATTAGTGTCGATGGAAAAGTGATCGG
++
+A/AAAEEEEEEEE/EE/E/EAEAEEEEEE/EEEA/AEEEAEEEEEE/EEEE/EEEEAEEEEE/E/A/AEEE/EEEEAEE//EEEEEEE/EEEEAE/EEEEEEEEEAEE/<//<EE/EEAEEEEEEEE6//EEEEEEEE/EEAE/AE/AA
+@NS500443:42:H3MH2AFXX:4:21612:11502:19343/2
+GTGTACGCGGTTTGCGAGTGCGGTCACCGCCACCAAAGTGTTTCTTGTGTTCTTTATCTTGTGATTTCTTTTCGTCTAACCCTGCAGGTTTCTCAAGCAAAGCTTTACGAGATAAATTGATCCGACCTTGGTTATCGATCTCGATCACTTT
++
+AAAAAEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEAEEEEEE/<EEEA<E</AEEE//EE<AEEE<AEEE<EEE6/<<<E</<
+@NS500443:42:H3MH2AFXX:4:21612:24968:19344/2
+ATTTTGCATAAGCGTCCCCTTCGCAAGAGGCGACCAAGCCGCATGAGCAATCCCATGTTTTTTCAGGAACGTTCGTAGTTCATTTTGTGGGAGAAGTGGATGCGTTTCTACTTGGTTAAGTACAGGTAATTCATTCGCAACGGCAAGCAAA
++
+AAAAAEEAEEAEEEEEEEEEEEEEEEEEEEEE/EE/EEEEEEAEE/EEEEEEEEEEEEEEEEEE/EE6AEEEEEE<EE/A/EAEEEEEEEE/E/AE6EE//EEE<E6A6AEEAAAEE<AEA///A<6/EAEE/EA<<E/AEEEE//EEE//
+@NS500443:42:H3MH2AFXX:4:21612:6916:19344/2
+GGCAACGACTTCGGCAGACTTACCATCAACGTTGACTTGATAATTCATTTTTCGCATTTCTGCATCCGTAATTTTCCCGGCCAGTTTATTTAGTGGGGCTTTCAGTTCAGGATACTTTTGCAATGTCTTAGTTAACATTAAAGGAGCGCC
++
+AAAA/EE/EEEEAEEEEAEAEEEEEEEEEEEE6E/EEEEEEEEEEE/AEEEEEEEEEEEEEEAEE/EE/EEEEEEEAEEEEEEAAAE/EAEEEA/AEEA/A<EAEA<<EEEEE/EAEA6AAE/<EAEAE6A6E<AEE<E/AAAEEEE<EE
+@NS500443:42:H3MH2AFXX:4:21612:15429:19346/2
+ATCTTTTAACTGATAGTAAAAATAAAGTTGTGGCACGCGGTACGAAGCAAGTTCAAGTAGCGACAGTCAGCCATGAAAATTCGAGTGAGAAAACTGTTGCAACAGCACCTGAGCAATCCAGTTCAGCATCAAGTAGCAGTAGTAGCGCAC
++
+AAAAAEEEEEEAEEEEEEAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEEEEEEEEE/EA/EEEEEEEEEEEEEE/EEEEE<AEAEAEEEEEEEEAEEEE/E/E
+@NS500443:42:H3MH2AFXX:4:21612:1024:19346/2
+GTATTATGGCTTACACAGTTTACAACATCGCGGGCAAGAAGGTGCGGGAATTGTTGCAACAGACGGCAAAGTGTTACGCGGGCACCGCAACTTAGGTTTGCTAGCAGATGTATTTAAACATGGGGAACTGGATGGTTTACCAGGAAGTGGG
++
+A6AAAAEEEAEEEEEEAEAEE/EEAEEEEEAEEEEEEEE6/EEEEEEEEEEEEEEEEEAE6E6E6EE/EEEEEEE/EEEEEEE/EAEE/EEE<AEE6EEE<EEEEAE/EEEEEEEEE/A/66EAE//EEAEA/<A/EEEAAA/EEAEEE</
+@NS500443:42:H3MH2AFXX:4:21612:4182:19348/2
+CCGTCAATCGGAAAGAACGCATATTTATGACCCGCTAATTGAACAACTTTTAGATGAAGGAAAAGCTTATAAATGTTATTGTACGGAAGAAGAACTAGAAGCAGAACGTGAAGCGCAAAAAGCCCGCGGTGAAATGCCTCGTTAGAGCGGA
++
+A/A/AEAEEEEEEEEE6EEEEEEEE/EEE6EEEEEEEEEEEE6AAEEAAEEAEEEE6EEAAE/EEEAEEEEEEEEEEA<6E<E/AEA/A/<EE/E/EEEEAE/E//E6EE//<AEE/E/A/<E/AAEEE6E////6E<//EA/<//A<E//
+@NS500443:42:H3MH2AFXX:4:21612:26730:19348/2
+ATCCACGAAACATCACAACACAAATGGCTAACTACGCATCTAAAACACTCAATTAAACAAAACCCGCACTCGAAAAGACTTATCCACTACCACCGATGGGAAAACCAGAAGACGTAACGAAGCACCATCACTTACAGCCTTCACATAAAT
++
+AAAA66EA6EEEE66E/EEAEE6/////AE/EE/EEE//E//E/EEEE/A/EEE/6AAEE/A//A//AEAA/////<EAE/E/EEEE//6E/A///AAEE/////<EE/E/E/<///EAE/E////<A<AEEA/E/A///6E/AEA////
+@NS500443:42:H3MH2AFXX:4:21612:25889:19349/2
+CTTTAGGATTAGAGGTGAGTGCTGGTAAAATTGAAGTAACGGGAATATTAATAGCCGAATAAAGAACTTTCGCGCCAATATAGGCGATATAAATCCATACAATTTTCGCTGTTTCGCTGCCCATAATAAAGCTTGGAGCTGAAAAAGCCAT
++
+AAAAAEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAEEEEEEEAEEEEEEEAEEEEEAEEEEAAAEEE/EEEEEEEEEA/AEEAEEAE<EEEEEEEAAEA6<EEEEEA/EEA<<AEAA<AEEEEEEEEEEAE<EEE<EEEEE
+@NS500443:42:H3MH2AFXX:4:21612:6539:19353/2
+GTATAAGGCGGACTATGAAAATGGACGGCTTCCACCTCAACGCCTCGCTTCATTGCTAAATAACCAGCTACTGGGCTATCAATTCCGCCAGATAGCATGAGCATTGCCTTTCCTGACGAACTAACAGGTAGCCCCCCAGCGCCTTGAATGA
++
+AAAAAEEE/EEAEEAEEEEEEEEEEEEEEAAEE/EE6EAEEEEEEEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEE/EEEEEEEEAAE/EEAEE/EEEEEEAEEEEEEAA/EE//E</<AEEE//AEEEEEE/EEEEE/EEEA<</
+@NS500443:42:H3MH2AFXX:4:21612:21998:19353/2
+TCTTTGCAGTCATCATATTTCACAGCAAATTCAATTGCGGCAATCCGGTCGAAGTAAGCGCTGTCAAGACGACGCATATTTCCCGGATCTTCTTTTGAATGGAGCCCTGTTTTTCCTTCAATTGCTTTCGTAAGATGGGTAAGTAAATCAA
++
+AAAAAEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEAEEAEEEEE<EEE6E6EEAEE/EEAEEEEEAEEAEEEEAEEAEEEAEAEEEEEA<AEEEEEEEA/AEEEEA<EE<E</EEEEE
+@NS500443:42:H3MH2AFXX:4:21612:9349:19354/2
+GGGCTTAATATGGCGATGGAACTAGCTCGAGCTGGCATTTTAGAAGAAATGAATGTCGAAGTCCTTGGAACAGATTTAAGAGCGTTTCAAAAAGCGGAAGATCGCGAAGAATTCCGGAACTTAATGAATGAGCTCGGGGAACCCGTCCCAG
++
+AAAAAE/EEEE/EEEEEEAEEEE/EEAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEA/<EEEA/E/E6E/AEEEEA/<EE//EEEEEEE/EEEEEEEAAE/EEAE/EE/6E/EA/EEAEEEAEAAEEEE/6EE/A/AEE///EE</
+@NS500443:42:H3MH2AFXX:4:21612:10100:19357/2
+ATTTGAAGAGTACCGGAAGCTTTATGAGTTTGATTATGGCGATTATGAACAGTCTAAGTGGGAAGCACACGTGAAAGTCCAAGCACGTCAGGAAATTGGCATTCGGCGCTTCTTAGAGGAAGGTGGATATAATGCCTTCACATCGAACTTT
++
+AAAAAEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEAEEEEEEEEEAE6AE
+@NS500443:42:H3MH2AFXX:4:21612:5905:19357/2
+GTGACGGGCTATGATATCACCGTAAAGAAAGTACTTGTACGCGATTTAGAAAAGAATCGCCGTTACGAGGCAGAAGGTTTTACCTTAACAACCGAACCAAAAGACGTGCTAGATGATCCAGAAATCGCTGTTATTGTAGAAGTAATGGGCA
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEA<EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEAEA
+@NS500443:42:H3MH2AFXX:4:21612:22823:19360/2
+GAAAACGGCAGCTTTATTTGGCCCGAAAACGTACAAGATTACGTTCAGTATTTCCACCGAATCGCAGCTGGCATCCTTGTTATTTGGATTTTATATGTGACTTGGCTCGTTTTCCGTGACTACAGACATTATCGCGTGTTAACGTATGGCA
++
+AAAA/EEEEEEEAEEAEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEAEEEEAEEEEEEAEEEEEE/EEEEEEEEEEEEEEEEEEE/EAAEEEEEEE<EEEEEEEAEAEEE/EEEEEEEEEEE/EE6EEEEEEE<E<A
+@NS500443:42:H3MH2AFXX:4:21612:17904:19360/2
+TCCTTGTAGCGCTTAAGCAAGAAATCCAGCAACGCGAAAGAATCCGGTCCTCCGGAAACTGCCACAAGCAATTTCTCATCTGGCCGGATTAAATCATGCTTTAGAATAAAGTTTTCGACACGCCTTGAAAATTCATCCATTCTAAAAAC
++
+AAAAAEEEEEEEE/EEEEEEEEE6AEE/EEAEEEEEE/EEEEEEEEEEEEEEEEEE/EEEEEEEEE/EAEEEEEEEEEEEEEAAEEEEEEEEEEEEEEE/EEEEEAEEEEEEAEAEE/EAEEE<EEAEEEEEE<EEEEE<AEEEEE//E
+@NS500443:42:H3MH2AFXX:4:21612:5361:19361/2
+ATACGGTGAAGCGAATGTTCAAAGAGATAAGACCTTACCTTATTCATTAAGGGATTTAATAAAGGTGGAAAAGAAAATTACTGTTCCTGCTAAAAAGAGTGTAGATTTGAAGTTAGCTGTTACTATGCCGGATAAACCATATGCGGGAGTA
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEAEEEEEEAEEEEEEEEAEEEAEEEEEEEAEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEAAEEEEEEEEEAEEEEEEEEEEEEEEEEEAEEEEE/
+@NS500443:42:H3MH2AFXX:4:21612:10976:19365/2
+CCATTAGGAGATCGTGTTGTTATTGAAGTAATTGAAGCAGAAGAAAAAACAGCGAGCGGCATCGTTTTGCCAGATTCGGCGAAAGAAAAACCGCAGGAAGGAAAGGTTGTTGCGGTAGGTTCTGGTCGTGTACTTGATAGTGGCACTAAAG
++
+AAAAAEEEEEAEEEEEEEEAE/EEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEAEEEEEEEEAEEEEEAA/EEEEEE6AEEEEAEEEEEEA/EEAEEEAE
+@NS500443:42:H3MH2AFXX:4:21612:22942:19365/2
+CGAAAAAACAAGCCGAACAAAATGCAGCGGAGTTTGCAGTTCGGCAGATGATGCATAAGTAGGAACGGAAGGAGAGAAGCAGTTTGCTATTAAAACGACTGGAAATGAATGGATTTAAATCATTTGCAGATAAAGTAGCAATTGATTTTGT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE6AEEEEEEAE/EEEAEEEEEEE<EAEEEEEEEEAEEAEEEEEEEEE//AE<AEEE<A
+@NS500443:42:H3MH2AFXX:4:21612:14114:19366/2
+AAATAAGGAAGCGTCATCGAGACATTCGCCATCAGCGTCAGTTTATTGTAGAAGGCAGAGGCATTGCTTCCGCCAAAAGAGGCGATCAAAATAATGACAACAACGATAAGACACTGAATCCACATTGCAAACTCTGGCATTCCTGCCTTGT
++
+AAAAAEEEEEEEEEEEEE6EEAEEEEEEEEEEEE6EEEEEEEEEAEEEAEEEAEEEEEEE6EEEEEEEEEEEEEEEEEE/EEEEEEEE<E/E/EEE/E/EEEEEEE/EEEEEEAEEEE/AEEEEEEEE///EEEEEEEAAAEEE/EEE/<<
+@NS500443:42:H3MH2AFXX:4:21612:13612:19370/2
+GATCAGGTTATGCAGATTTTTAATATCGAAGCAGATGTAGATTTAGATATTATGAAAGCAGGTCAAACGCTAAGTGATATAACATCACGAGTTTTATCTGGTCTAGTCGAAACAATCAAGCAGGAACAACCAGACATTGTGCTTGTCCACG
++
+AAAAAEEEEEEEEEEAEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEE<EEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEAEEA<AEEE<EEEEEEEEE<E<<EEEE
+@NS500443:42:H3MH2AFXX:4:21612:1049:19371/2
+CTCCCTCACCGGCGCGCTTTAATTCTCGTAACACAAAAAATTGTTCCGTTGAAATTCGCTTTCCGCCAATCTCCACTTCTTCAATCGCTTGATCAATTTCTTTTAATGCAAATAAATACGTCCGTGTATAACCATCAATAAAGCGATCTAA
++
+AAAAAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEAE<EEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAAEEEEAEEEEAEEEEEEEEEEEEEEEAEEE/
+@NS500443:42:H3MH2AFXX:4:21612:9601:19373/2
+CTATTTGCATGAGCGAATGACTTGGACTGCTTATAAGCTCTTTTATTTGCGGAAAAAGCGAAACTTGCAAAATGATTCAGAACGATTGCAATATATGGATGAAGCGCTGACTGAAATTGGGAAATTAAGCCAAGCGGTTGAGCGTGAACTT
++
+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEE/EEEEAEEEEEAEEEAEEAE///EEEEEEEEEEAE<AEEEEEEEAEEEEEEEEA
+@NS500443:42:H3MH2AFXX:4:21612:20393:19375/2
+GTCTCAAGCGACTTGATCAGTGGTTCAAAATGATGATTTTGACTTATTTTCCCGTAAAGAGTGACTTCATCCCCATTGACTGCAATCACGTTTTCTTCACTAAAACCTTGGCTGAATGTTCCAGTTGCAGAATCGGATAATTTAACGCCTA
++
+AAAAAEEEEE/E/EEEEEEEEE6EEEEEEEEEEEEAEEEEE/AEAEAEEEEEE6AEEEEAEEE/EEEE/EEE/EEEAEEEE6EEAAEA//A/<E/6/EEEAEEE<AAEA/AA/AE/A/<EE/A/<AE/AAE/EE/EE/EEE/EE/AEEEAE
+@NS500443:42:H3MH2AFXX:4:21612:18713:19376/2
+GCTTATATCCCAACAAATGTAATCTCCATAACTGACGGACAGATTTTCTTACAGTCTGATTTGTTCTTCTCTGGGGTTCGTCCAGCGATTAATGCTGGTTTATCTGTATCACGTGTTGGTGGTTCCGCACAAATCAAAGCAATGAAGAAAG
++
+AAAAAEEEEEEEEEEEEEEEE/EEEEEEEEEAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEA<EEEEEEEEEAEAEEEEAEE6EEA<EAEEEEEEEEEE/AEE/EEEE/AA/AE
+@NS500443:42:H3MH2AFXX:4:21612:16612:19377/2
+CTTGATGATGACTTTAATCAATTCCTTCTTAGTGTGCGTTCGAAAAGTGTTAAATGGATAAAGGAACAGATGCTACTAGTATATGGGAAAGATACCGAACCTTATTTGAATGATCTTGCAATGATGTTAACGGGAATGATTCTTCTTTTTG
++
+AAAAAEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEAEEE/EEEE/EEEEEEE/AEEEEEEEEAEEEEEEEEEAEEE/EEEAEAE<EEAEAAEEEEE/
+@NS500443:42:H3MH2AFXX:4:21612:21100:19378/2
+GCCCAGAACCAATCACTGCAATTTTTTTATCCCACCGCACTATCGGTGGAGTCGGCATGAACCAACCTAAACCAAACCCACGGTCAATAATAGCCCGTTCAATCGAATTAATACCCACAGCAGGATCAGAAATTGCAACCGTACAACTTC
++
+AAAAAE/E/EEEEEEAAAEEE////EEE/AEA/////E/////E//E66EA/AEEE/EEE//////AE////AEA/EE//AE/EE/EEEEE//E/E//EEAAA//A/EEE/A/A/6A</A///E/EAE/E<A//E//////6/E///6<<
diff --git a/src/FqAuxBackend.cpp b/src/FqAuxBackend.cpp
index 26912250b7e89aa6cc47f66329b976f637bd2013..ef58d76807b11edfefc8444d77a6a54e64538623 100644
--- a/src/FqAuxBackend.cpp
+++ b/src/FqAuxBackend.cpp
@@ -13,6 +13,7 @@
#include <errno.h>
#include <err.h>
#include <stdlib.h>
+#include "FqBaseBackend.h"
#include "FqAuxBackend.h"
@@ -125,8 +126,8 @@ int FqAuxBackend::processBuffer(rinfo * p_nr) {
void FqAuxBackend::readBuffer() {
- if ((nread=read(f_pe2,buf,bufsize))!=0) {
- cur_offset=ftell(fp2);
+ if ((nread=read(f_desc,buf,bufsize))!=0) {
+ cur_offset=ftell(f_stream);
pos_in_buf=0;
}
}
@@ -134,37 +135,20 @@ void FqAuxBackend::readBuffer() {
* Opens file and performs the fist read operation.
*/
void FqAuxBackend::openFile(char * ficname, unsigned char id) {
- int st,s;
- // unsigned long cur_offset;
- mode_t mode = S_IRUSR | S_IWUSR | S_IRGRP | S_IROTH;
-
- closeFile();
- filename=ficname;
- f_id=id;
-
- f_pe2=open(filename,O_RDONLY,mode);
- if (f_pe2==-1) {
- err(errno,"cannot open file: %s.",filename);
- }
-
- fp2=fdopen(f_pe2,"r");
- if (fp2==NULL) {
- err(errno,"cannot open file: %s.",filename);
- }
- buf=(char *) malloc(bufsize*sizeof(char));
- if (buf==NULL) {
- err(errno,"cannot allocate memory: %lu bytes.",bufsize);
- }
- pos_in_buf=bufsize; // do that to force first reading in buffer.
+ FqBaseBackend::openFile(ficname,id);
+ buf=(char *) malloc(bufsize*sizeof(char));
+ if (buf==NULL) {
+ err(errno,"cannot allocate memory: %lu bytes.",bufsize);
}
+ pos_in_buf=bufsize; // do that to force first reading in buffer.
+}
void FqAuxBackend::closeFile() {
- if (filename!=NULL) {
- close(f_pe2);
- filename=NULL;
- free(buf);
- buf=NULL;
- }
+ if (filename!=NULL) {
+ FqBaseBackend::closeFile();
+ free(buf);
+ buf=NULL;
}
+}
diff --git a/src/FqAuxBackend.h b/src/FqAuxBackend.h
index badb2ee563ba93f36bef92477f88ba4cf08f6875..b52805d9e7b7ef02108106fb4b792cdb06e5b7c0 100644
--- a/src/FqAuxBackend.h
+++ b/src/FqAuxBackend.h
@@ -9,15 +9,13 @@
#define FQAUXBACKEND_H_
#include "srp.h"
+#include "FqBaseBackend.h"
+
const size_t bufsize=6048000; // It seems that I can't have a much bigger value than that or else my objects construction throws exception. Strange.
// const size_t bufsize=500000; //try that in valgrind
-class FqAuxBackend {
- char * filename;
- unsigned char f_id;
+class FqAuxBackend:public FqBaseBackend {
size_t nread;
- int f_pe2; // for calling read
- FILE * fp2; // for calling ftell
unsigned long cur_offset;
char * buf;
@@ -30,17 +28,12 @@ public:
char current_id[50];
FqAuxBackend() {
- filename=NULL;
- f_pe2=-1;
- fp2=NULL;
- f_id=0;
cur_offset=0;
nread=0;
buf=NULL;
+ pos_in_buf=bufsize;
}
-
void openFile(char * ficname, unsigned char id);
-
void closeFile();
int getNextRead(rinfo *);
diff --git a/src/FqBaseBackend.cpp b/src/FqBaseBackend.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..73d4ba9c6482c474b411fb90e24a21399627f112
--- /dev/null
+++ b/src/FqBaseBackend.cpp
@@ -0,0 +1,75 @@
+/*
+ * FqBaseBackend.cpp
+ *
+ * Created on: Jan 20, 2016
+ * Author: vlegrand
+ */
+//#include <stdio.h>
+#include <fcntl.h>
+//#include <stdlib.h>
+#include <unistd.h>
+#include <errno.h>
+#include <err.h>
+
+#include "FqBaseBackend.h"
+
+
+void FqBaseBackend::openFile(char * ficname, unsigned char id) {
+ int st,s;
+ // unsigned long cur_offset;
+ mode_t mode = S_IRUSR | S_IWUSR | S_IRGRP | S_IROTH;
+
+ closeFile();
+ filename=ficname;
+ f_id=id;
+
+ f_desc=open(filename,O_RDONLY,mode);
+ if (f_desc==-1) {
+ err(errno,"cannot open file: %s.",filename);
+ }
+
+ f_stream=fdopen(f_desc,"r");
+ if (f_stream==NULL) {
+ err(errno,"cannot open file: %s.",filename);
+ }
+}
+
+void FqBaseBackend::closeFile() {
+ if (filename!=NULL) {
+ close(f_desc);
+ filename=NULL;
+ f_desc=-1;
+ f_stream=NULL;
+ /*free(buf);
+ buf=NULL;*/
+ }
+}
+
+/*
+ * use C style char* rather than std::string for a matter of performance.
+ * use read instead of fread for the same reason.
+ *
+ * Note: It is up to the caller to determine where the end of the record is (5th \n character in the fq_record string).
+ */
+void FqBaseBackend::getRead(const long& offset, char * fq_record) {
+
+
+ //char fq_record[MAX_FQ_RECORD_LENGTH];
+
+ int nread,i,nb_lines;
+ char * pchar;
+
+ if (f_desc==-1) err(0,"No open file currently associated to this backend");
+ // if (f_stream==NULL) err(0,"No open file currently associated to this backend");
+
+ int res=lseek(f_desc,offset,SEEK_SET);
+ if (res==-1) err(errno,"fseek problem when trying to retrieve dna string.");
+ nread=read(f_desc,fq_record,MAX_FQ_RECORD_LENGTH);
+/*
+ i=0;
+ pchar=fq_record;
+ while (i<=nread-1) {
+
+ }*/
+
+}
diff --git a/src/FqBaseBackend.h b/src/FqBaseBackend.h
new file mode 100644
index 0000000000000000000000000000000000000000..a5bec4a0c9fd75da9b67ea691f7f788debde969d
--- /dev/null
+++ b/src/FqBaseBackend.h
@@ -0,0 +1,43 @@
+/*
+ * FqBaseBackend.h
+ *
+ * Created on: Jan 20, 2016
+ * Author: vlegrand
+ */
+
+#ifndef FQBASEBACKEND_H_
+#define FQBASEBACKEND_H_
+
+#include "FqConstants.h"
+#include "srp.h"
+
+
+
+
+class FqBaseBackend {
+
+ // TODO: this class will also be associated to writing output "filtered" fastq files.
+
+protected:
+ char * filename;
+ unsigned char f_id;
+ int f_desc; // for calling read
+ FILE * f_stream; // for calling ftell
+
+public:
+
+ FqBaseBackend() {
+ filename=NULL;
+ f_desc=-1;
+ f_stream=NULL;
+ f_id=0;
+ }
+
+ void openFile(char * ficname, unsigned char id);
+ void closeFile();
+ void getRead(const long&,char *);
+};
+
+
+
+#endif /* FQBASEBACKEND_H_ */
diff --git a/src/FqConstants.h b/src/FqConstants.h
index e41463a17efac020316b8347839baf4ee6f7df9f..1fb1ea6b878d7678200e6f7fcf9f73b42054edaf 100644
--- a/src/FqConstants.h
+++ b/src/FqConstants.h
@@ -12,4 +12,10 @@
#define k_read_qual_start '+'
#define k_phred_32 33
+const unsigned char mask=0x0F; // used to retrieve file identifier in the case of PE reads.
+
+#define MAX_READ_LENGTH 3000 // set this arbitrary for the moment. This will likely become a parameter of the program later.
+
+#define MAX_FQ_RECORD_LENGTH 3000
+
#endif /* FQCONSTANTS_H_ */
diff --git a/src/FqMainBackend.cpp b/src/FqMainBackend.cpp
index 30ae15071c4d0747bfa0ff1e1520fd9d3b25b83b..d79f22de1064695cf50dd021abf238f49cf0e8f6 100644
--- a/src/FqMainBackend.cpp
+++ b/src/FqMainBackend.cpp
@@ -15,31 +15,16 @@
#include <assert.h>
#include <stdlib.h>
-// for debug only. TODO : remove that.
+//#define DEBUG
+
+#ifdef DEBUG
#include <iostream>
using namespace std;
+#endif
#include "FqMainBackend.h"
#include "srp.h"
-//#define DEBUG
-
-rpos init_rpos(unsigned char f_id, unsigned long rstart_offset) {
- rpos rp;
- rp.fileid=f_id <<4;
- rp.read_a1=rstart_offset%INT_MAX;
- return rp;
-}
-
-/*
- * Add Paired read information to already existing rpos structure.
- */
-void update_rpos(unsigned char f_id,unsigned long rstart_offset,unsigned long j, rpos * rp) {
- rp->fileid=rp->fileid|f_id;
- rp->read_a2=rstart_offset-INT_MAX*j;
-}
-
-
FqMainBackend::FqMainBackend(srp * io_sr) {
p_auxFqProcessor=NULL;
@@ -87,8 +72,6 @@ void FqMainBackend::processFile(char * filename,unsigned char f_id) {
void FqMainBackend::processBuf(char * buf,int nread,unsigned char f_id,unsigned long cur_offset) {
int cnt=0;
- // debug stuff, TODO: remove it
- // static int nb_read_PE1=0;
unsigned int s;
static unsigned int st;
static int num_l_in_rec; /* counter to know on which line inside the fastq record we are */
@@ -133,7 +116,6 @@ void FqMainBackend::processBuf(char * buf,int nread,unsigned char f_id,unsigned
// std::cout<<"BE1 position in buffer "<<cnt+1<<endl; //add 1 to compare value with BE2.
qual_score=0;/* end of fastq record */
rpos rp=init_rpos(f_id,rstart_offset);
- // nb_read_PE1++; // TODO: remove, this is debug stuff
if (p_auxFqProcessor!=NULL) {
rinfo pe2info;
int eof=p_auxFqProcessor->getNextRead(&pe2info);
diff --git a/src/FqMainBackend.h b/src/FqMainBackend.h
index 38a9bf30f70da4f1b823c018c89f8a535917dadf..c8b2b1aab351014426b87c256cf3119207987693 100644
--- a/src/FqMainBackend.h
+++ b/src/FqMainBackend.h
@@ -10,11 +10,13 @@
#ifndef FQMAINBACKEND_H_
#define FQMAINBACKEND_H_
+#include "FqBaseBackend.h"
#include "FqAuxBackend.h"
#include "FqConstants.h"
-class FqMainBackend {
+
+class FqMainBackend : public FqBaseBackend {
FqAuxBackend * p_auxFqProcessor; /* Another fastq processor component is necessary for handling the case of PE reads.*/
srp * p_scoreReadStruct; /* Where we store information about the reads. */
char current_id[50];
diff --git a/src/Makefile.am b/src/Makefile.am
index 6763ca1aa7b40c095d98e690d0768270db99cb38..631aeea2b7ca59e68be5d9acaaed610433c11cf8 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -3,7 +3,8 @@ LINTDEFS = $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS)
AM_CPPFLAGS = -DDATADIR=\"$(pkgdatadir)\"
bin_PROGRAMS=rock
-noinst_PROGRAMS = unit_test_fqreader
+noinst_PROGRAMS = unit_test_fqreader perf_test_fqreader
+## noinst_PROGRAMS =
noinst_LIBRARIES = librock.a
noinst_HEADERS = $(HDR)
@@ -14,7 +15,10 @@ rock_LDADD = librock.a
unit_test_fqreader_SOURCES=unit_test_fqreader.cpp
unit_test_fqreader_LDADD=librock.a
+perf_test_fqreader_SOURCES=perf_test_fqreader.cpp
+perf_test_fqreader_LDADD=librock.a
+
librock_a_SOURCES = $(SRC)
-SRC = fqreader.cpp FqAuxBackend.cpp FqMainBackend.cpp
-HDR = srp.h fqreader.h FqConstants.h FqAuxBackend.h FqMainBackend.h
\ No newline at end of file
+SRC = fqreader.cpp FqBaseBackend.cpp FqAuxBackend.cpp FqMainBackend.cpp read_utils.cpp
+HDR = srp.h fqreader.h FqConstants.h FqBaseBackend.h FqAuxBackend.h FqMainBackend.h rock_types.h read_utils.h
\ No newline at end of file
diff --git a/src/fqreader.cpp b/src/fqreader.cpp
index 7b8169f1536e35aba574015fc8e20199c18b3dc9..3615555a2a9f07eb6af60e45f9d7f9a107564758 100644
--- a/src/fqreader.cpp
+++ b/src/fqreader.cpp
@@ -18,20 +18,6 @@
-
-/*
-typedef struct {
- char buf[bufsize];
- unsigned char f_id;
- int nread;
- unsigned long cur_offset;
-}fastq_buf;*/
-
-
-
-
-
-
/*
* Processes 1 file containing single reads
*/
@@ -52,9 +38,34 @@ void processPEFiles(char * fq_1, unsigned char f_id1,char * fq_2, unsigned char
}
/*
- * This function processes the content of an rpos structure and returns the character string "ATCG" corresponding to the read record.
+ * This function processes the content of an rpos structure and returns the character string "ATCG..." corresponding to the read record.
* PE reads are concatenated.
*/
-void getRead(char ** fname_id_array, const rpos& sr, unsigned int j, char ** dna_read){
-}
+/*void getRead(fq_file_map& fic_map,const rpos& sr, unsigned int j, char * dna_read){
+ unsigned char f_id1;
+ unsigned char f_id2=2;
+ int is_PE=0;
+ f_id1=sr.fileid >>4;
+ f_id2=sr.fileid &mask;
+
+ if (f_id2!=0) is_PE=1;
+
+ fq_file struc_f1=fic_map[f_id1];
+ if (is_PE) fq_file struc_f2=fic_map[f_id2];
+
+ if (struc_f1.fic_desc==0) { // file is not yet open
+ struc_f1.fic_desc=open(filename,O_RDONLY,mode);
+ if (f_pe2==-1) {
+ err(errno,"cannot open file: %s.",filename);
+ }
+
+ fp2=fdopen(f_pe2,"r");
+ if (fp2==NULL) {
+ err(errno,"cannot open file: %s.",filename);
+ }
+
+ }
+
+
+}*/
diff --git a/src/fqreader.h b/src/fqreader.h
index bd823d944facebd88ffdf2ebe43d2b4fe4516925..f5f0eb1266785671541e1445b1cd4216f441b487 100644
--- a/src/fqreader.h
+++ b/src/fqreader.h
@@ -8,11 +8,9 @@
#define FQREADER_H
#include "srp.h"
-const int read_length=1000; // this will become a parameter later.
-
/*void processBuf(char * buf,int nread,int cur_offset);*/
void processSingleFile(char *, unsigned char, srp*);
void processPEFiles(char * fq_1, unsigned char f_id1,char * gq_2, unsigned char f_id2,srp *io_sr );
-void getRead(char ** fname_id_array, const rpos& sr, unsigned int j, char ** read);
+// void getRead(fq_file_map&, const rpos& sr, const unsigned int& j, char * read);
#endif
diff --git a/src/read_utils.cpp b/src/read_utils.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..79e6808d1530266f8853b29d2b2580d478c91d33
--- /dev/null
+++ b/src/read_utils.cpp
@@ -0,0 +1,82 @@
+/*
+ * read_utils.c
+ *
+ * Created on: Jan 20, 2016
+ * Author: vlegrand
+ * * Utility methods for processing DNA reads : decomposition in overlapping k-mers, converting a k-mer into a number,
+ * reverse complement and so on...
+ */
+
+/*
+ * This function processes the content of an rpos structure and returns the character string "ATCG..." corresponding to the read record.
+ * PE reads are concatenated.
+ */
+#include "FqConstants.h"
+#include "rock_types.h"
+#include "srp.h"
+#include "read_utils.h"
+
+void getFqRecord(FqBaseBackend* fq_files_be[],const unsigned char& f_id,const long& offset,
+ char * fq_record) {
+ FqBaseBackend * be=fq_files_be[f_id];
+ be->getRead(offset,fq_record);
+}
+
+
+void init_DnaSeqStr(DnaSeqStr * dna_seq) {
+ dna_seq->fq_record_buf[0]='\0';
+ dna_seq->length=0;
+ dna_seq->start_idx=0;
+}
+
+void processFqRecord(DnaSeqStr * dna_seq) {
+ char * pchar=dna_seq->fq_record_buf;
+ int cnt=0;
+ int nb_l=0;
+#ifdef DEBUG
+ assert(*pchar==k_read_id_start);
+#endif
+ while (cnt<=MAX_FQ_RECORD_LENGTH-1) {
+ if (*pchar=='\n') {
+ nb_l++;
+ if (nb_l==1) dna_seq->start_idx=cnt+1;
+ if (nb_l==2) {
+ dna_seq->length=cnt-dna_seq->start_idx;
+ break;
+ }
+ }
+ pchar++;
+ cnt++;
+ }
+#ifdef DEBUG
+ assert(nb_l>=2);
+#endif
+}
+
+
+void getDNASeqstr(FqBaseBackend* fq_files_be[],
+ const rpos& sr,
+ unsigned int j,
+ DnaSeqStr * dna_seqs)
+{
+ unsigned char f_id1;
+ unsigned char f_id2;
+ DnaSeqStr * p_dna_seqs=dna_seqs;
+
+ unsigned char fid_stored=sr.fileid;
+
+ f_id1=fid_stored >>4;
+ f_id2=fid_stored &mask;
+
+ long offset1=j*INT_MAX+sr.read_a1;
+ getFqRecord(fq_files_be,f_id1,offset1,dna_seqs[0].fq_record_buf);
+ processFqRecord(p_dna_seqs);
+
+ if (f_id2!=0) { // case of PE reads.
+ p_dna_seqs+=1;
+ long offset2=sr.read_a2+j*INT_MAX;
+ getFqRecord(fq_files_be,f_id2,offset2,dna_seqs[1].fq_record_buf);
+ processFqRecord(p_dna_seqs);
+ }
+
+}
diff --git a/src/read_utils.h b/src/read_utils.h
new file mode 100644
index 0000000000000000000000000000000000000000..6bde5d3ecb4999312fe2c8e8560523768113a59b
--- /dev/null
+++ b/src/read_utils.h
@@ -0,0 +1,33 @@
+/*
+ * read_utils.h
+ *
+ * Created on: Jan 20, 2016
+ * Author: vlegrand
+ */
+
+#ifndef READ_UTILS_H_
+#define READ_UTILS_H_
+
+#include "FqConstants.h"
+#include "rock_types.h"
+
+/*
+ * Here, for performance matters, do not want to have to do a memmove nor strcpy or strcat to extract only DNA sequence for all
+ * the fastq records that we'll have to process (potentially millions). So, use a structure to store start position of DNA sequence in buffer and its length.
+ * We will not process more than 2 fastq records at a time (case of he PE reads) so it will not take too much space in memory.
+ */
+
+typedef struct {
+ char fq_record_buf[MAX_FQ_RECORD_LENGTH];
+ int start_idx;
+ int length;
+}DnaSeqStr;
+
+void getDNASeqstr(FqBaseBackend* [],
+ const rpos&,
+ unsigned int,
+ DnaSeqStr *);
+
+void init_DnaSeqStr(DnaSeqStr * dna_seq);
+
+#endif /* READ_UTILS_H_ */
diff --git a/src/rock.cpp b/src/rock.cpp
index dea30b58558f02e3ce68eddadee5de87274693a6..5cfb275d6c491835ecf093ffcb819ad550017058 100644
--- a/src/rock.cpp
+++ b/src/rock.cpp
@@ -16,7 +16,7 @@
#include <err.h>
#include <string.h>
-#include "srp.h"
+// #include "srp.h"
#include "fqreader.h"
#define k_max_input_files 15
diff --git a/src/rock_types.h b/src/rock_types.h
new file mode 100644
index 0000000000000000000000000000000000000000..fe80bac75f833b822b98c723fa7dfcbb596c7c8a
--- /dev/null
+++ b/src/rock_types.h
@@ -0,0 +1,29 @@
+/*
+ * rock_types2.h
+ *
+ * Created on: Jan 20, 2016
+ * Author: vlegrand
+ * Gather here typedefs and structures useful for the main program and "inter-modules" data exchange.
+ * I divided rock into 4 "modules":
+ * 1- fqreader (parses fastq and fills 3D array of structures reprensenting all reads).
+ * 2- read-utils (utility functions for DNA reads processing)
+ * 3- CMS (fill and use).
+ * 4- fqwriter (writes fq filtered by CMS).
+ */
+
+#ifndef ROCK_TYPES_H_
+#define ROCK_TYPES_H_
+
+#include <map>
+#include "FqBaseBackend.h"
+
+/*typedef struct {
+ FqBaseBackend& fq_be;
+
+}fq_io;*/
+
+// typedef std::map<unsigned char,FqBaseBackend&> fq_file_map;
+
+#define k_max_input_files 15
+
+#endif /* ROCK_TYPES_H_ */
diff --git a/src/srp.h b/src/srp.h
index 488cd23e05825bf54aaaa11a988b72c7825eb874..b4b2b22d2743ad1a52305fe64d7f73af0a141990 100644
--- a/src/srp.h
+++ b/src/srp.h
@@ -20,9 +20,6 @@ typedef struct { /* Here store read offset in files whose ids are stored in the
}rpos;
-
-
-
typedef struct {
unsigned int score; // total quality score for read.
unsigned long rstart_offset; // read offset in file
@@ -34,4 +31,20 @@ typedef std::map<unsigned long,k_dim> i_dim;
typedef std::map<unsigned long,i_dim> srp;
+inline rpos init_rpos(unsigned char f_id, unsigned long rstart_offset) {
+ rpos rp;
+ rp.fileid=f_id <<4;
+ rp.read_a1=rstart_offset%INT_MAX;
+ return rp;
+}
+
+/*
+ * Add Paired read information to already existing rpos structure.
+ */
+inline void update_rpos(unsigned char f_id,unsigned long rstart_offset,unsigned long j, rpos * rp) {
+ rp->fileid=rp->fileid|f_id;
+ rp->read_a2=rstart_offset-INT_MAX*j;
+}
+
+
#endif /* SRP_H_ */
diff --git a/src/unit_test_fqreader.cpp b/src/unit_test_fqreader.cpp
index 64160bd84da0ceb0180be6714267a6ed1ffb1145..41887435bd5b10b1f0793912931462eefd27be5d 100644
--- a/src/unit_test_fqreader.cpp
+++ b/src/unit_test_fqreader.cpp
@@ -11,9 +11,12 @@
#include <limits.h>
#include <assert.h>
#include <stdlib.h>
+#include "FqConstants.h"
#include "srp.h"
#include "fqreader.h"
+// TODO : Add test case where @ character is inside quality score.
+
using namespace std;
void test_processSingleFile() {
@@ -146,13 +149,132 @@ void test_processAllFiles() {
assert(cnt_read==9);
}
+#include "read_utils.h"
+#include "rock_types.h"
+#include "FqMainBackend.h"
+//#include "srp.h"
+
+void test_getReadSingle() { // TODO : move this to another test file.
+ rpos my_struct1,my_struct2;
+ my_struct1=init_rpos(4,639);
+ my_struct2=init_rpos(4,1228);
+
+ //std::cout<<my_struct1.read_a1<<endl;
+
+ assert(my_struct1.read_a1==639);
+ assert(my_struct2.read_a1==1228);
+ srp io_sr;
+ unsigned int j=0;
+ DnaSeqStr a_seqs;
+ char dna_read[MAX_READ_LENGTH];
+
+ char * fq_single2=(char *) "../data/test_single2.fq";
+ FqMainBackend be_fq=FqMainBackend(&io_sr); // TODO, remove argument from constructor
+ be_fq.openFile(fq_single2, 4);
+
+
+ FqBaseBackend * fic_map[k_max_input_files];
+ fic_map[4]=&be_fq;
+
+ init_DnaSeqStr(&a_seqs);
+ getDNASeqstr(fic_map, my_struct1, 0, &a_seqs);
+ char * tmp=(char *) a_seqs.fq_record_buf;
+ tmp+=a_seqs.start_idx;
+ memcpy(dna_read,tmp,a_seqs.length);
+ // std::cout<<dna_read<<endl;
+ assert(strcmp(dna_read,"TTTTTAGGTGCTACCATAACACCAACTGTTTTCACCATAATTTTAAAATCAAGCATTAGAGACGCTTCTCTAATGTATTGCAAATCTAGTTCTACCATTTGATGAAAATCTAATTCATTTCTTCCACTAACCTGCCATAATCCAGTACAACCTGGTATAACGGTCAAACGCTTTTTATCATAGGAACTGTATTCTCCTACCTCACGTGGCAAAGGAGGTCTTGGACCAACAATTGCCATGTCTCCTTTAACCACATTCCAAAGCTGTGGTA")==0);
+
+
+ init_DnaSeqStr(&a_seqs);
+ assert(strcmp(a_seqs.fq_record_buf,"")==0);
+ assert(a_seqs.length==0);
+ assert(a_seqs.start_idx==0);
+
+ getDNASeqstr(fic_map, my_struct2, 0, &a_seqs);
+ tmp=(char *) a_seqs.fq_record_buf;
+ tmp+=a_seqs.start_idx;
+ memcpy(dna_read,tmp,a_seqs.length);
+ if (a_seqs.length<MAX_READ_LENGTH) dna_read[a_seqs.length]='\0';
+ std::cout<<dna_read<<endl;
+ assert(strcmp(dna_read,"ACCCAAACTTGCCAGACTTGTGTAGAACGTCCAATATGTATCGGCATCGCTTCCACATGAATGAATCCTTGTTCCACACTTTTTATATGATTCGCATTAATTTCTTGTCCGAAAATCAACTGATTTTTTGCAACATTTTCTCCCGCTCCAAGACTGGCTGCATGTTCTGCAAGCGCAACAGAAACACCACCATGCAAGTAGCCAAAGGGTTGTTTGACCTGATCTGTTATTTCAAGCGCCAGTTCCACTC")==0);
+ be_fq.closeFile();
+}
+
+void getDnaStr(FqBaseBackend * fic_map[],rpos my_struct,DnaSeqStr* a_seqs,char * dna_read) { // Auxilliary method for test_getReadPE().
+ getDNASeqstr(fic_map, my_struct, 0, a_seqs);
+
+ char * tmp=(char *) a_seqs[0].fq_record_buf;
+ tmp+=a_seqs[0].start_idx;
+
+ memcpy(dna_read,tmp,a_seqs[0].length);
+
+ tmp=(char *) a_seqs[1].fq_record_buf;
+ tmp+=a_seqs[1].start_idx;
+
+ char * b=(char *) dna_read+a_seqs[0].length;
+ memcpy(b,tmp,a_seqs[1].length);
+
+ if (a_seqs[0].length+a_seqs[1].length<MAX_READ_LENGTH) dna_read[a_seqs[0].length+a_seqs[1].length]='\0';
+}
+
+void test_getReadPE() { // TODO: move this function to a separate test file : unit_tests_read_uils.cpp when I will have enough tests for this component.
+ rpos my_struct1,my_struct2;
+ char * fq_PE1=(char *) "../data/test_PE1_2.fq";
+ char * fq_PE2=(char *) "../data/test_PE2_2.fq";
+ srp io_sr;
+ unsigned int j=0;
+ char dna_read[MAX_READ_LENGTH];
+
+ FqMainBackend be_fq1=FqMainBackend(&io_sr);
+ FqAuxBackend be_fq2;
+ be_fq1.setAuxProcessor(&be_fq2);
+
+ be_fq1.openFile(fq_PE1, 4);
+ be_fq2.openFile(fq_PE2, 4);
+
+ FqBaseBackend * fic_map[k_max_input_files];
+ fic_map[4]=&be_fq1;
+ fic_map[5]=&be_fq2;
+
+ DnaSeqStr a_seqs[2];
+
+ init_DnaSeqStr(&a_seqs[0]);
+ init_DnaSeqStr(&a_seqs[1]);
+
+ my_struct1=init_rpos(4,0);
+ update_rpos(5,0,j,&my_struct1);
+
+ my_struct2=init_rpos(4,13648);
+ update_rpos(5,13654,j,&my_struct2);
+
+ assert(my_struct1.read_a1==0);
+ assert(my_struct1.read_a2==0);
+ assert(my_struct2.read_a1==13648);
+ assert(my_struct2.read_a2==13654);
+
+ getDnaStr(fic_map,my_struct1,a_seqs,dna_read);
+ std::cout<<dna_read<<endl;
+
+ assert(strcmp(dna_read,"GGTTCTGTTGGCTCAAACGCCGTCACTTCATTGATCAAAAGCTTATAATGCGTGCCAAAGTCCGCCATCGAGACGACTACGCCTTCCCCTGCTTTCCCGTCAAAAACGAGTCTTGCCGGATCTTCACGGTCTCCCCTCGAAAGCGGCGAAATCTTAGAGGAAGGTGGATATAATGCCGTCACATCGAACTTTGAAGATCTATACGGCATGCAGCAGCTTCCAGGTCTTGCGGTGCAACGTTTAATGGCAGATGGCTACGGTTTTGCGGGGGAAGGAGACTGGAAAACGGCGGCGATCGACCG")==0);
+
+ getDnaStr(fic_map,my_struct2,a_seqs,dna_read);
+ assert(strcmp(dna_read,"ATTGTGGGGTTCCTTTTTGTAGCATTGGAATGGAAATTAAAAATGGGGCTTCAGGATGCCCGCTCCATTATTTAATTCCAGAATGTAACGATGCTGTTTACCGGGGGGACTGGAAAGATGCACTTGAGCTTTTGATTAAAACAAATAACATGCCCAGAACCAATCACTGCAATTTTTTTATCCCACCGCACTATCGGTGGAGTCGGCATGAACCAACCTAAACCAAACCCACGGTCAATAATAGCCCGTTCAATCGAATTAATACCCACAGCAGGATCAGAAATTGCAACCGTACAACTTC")==0);
+
+ be_fq1.closeFile();
+ be_fq2.closeFile();
+ cout<<"done"<<endl;
+
+}
+
int main(int argc, char **argv) {
- cout<<"sizeof(char)"<<sizeof(char);
- /*char* fq_s_test="data/test_single.fq";*/
cout<<"test for single file"<<endl;
test_processSingleFile();
cout<<"test for PE files"<<endl;
test_processPEFiles();
- cout<<"test for both single and PE files";
+ cout<<"test for both single and PE files"<<endl;
test_processAllFiles(); /* mix PE together with single; nearly as in real life.*/
+ cout<<"test getting single reads."<<endl;
+ test_getReadSingle();
+ cout<<"test getting PE reads."<<endl;
+ test_getReadPE();
}