Re: [Seqan-dev] Fastq test files

[Theodore Omtzigt <theo@stillwater-sc.com>]

Manuel: using your pointer that Dna/Dna5 discrepancies will error, I was able to found the error: the files contain a couple of records that contain 'N' characters: making the shortReads a seqan::String<Dna5> solves our problem.

SeqAn is AWESOME!

...
@:89:A0172:1:1:24794:29480 1:N:0:1
CTTAAAAACATACCGTGTCCCCCGAGCTGTACCATTCCTGCTTCAAAAGATACGCGAGTACGAGTTGAATGTTTATCAAAGATAAGCCCTAATATTTTGCCTTGCAGTAAAGGCTCTTGCTTATTCTTTTTTAAATATATTGCGAACTCAA
+
CCCFFFFFGHHHHJJIGIIIIJJJJJJJFGHIIJFIJJJJJIJJJIJJEIIIIGIJHF>BACDDD@@>CCA:>ADDCEDACDDDDCCCDDDDDDDD>C@CCDD:@@CCCD<@:?:?AC@@C::@DEEDCDDDDDCADDC:B:399@>B>:+
@:89:A0172:1:1:18943:29511 1:N:0:1
ATTCTTGATTGTCCGATACCACCGCCAATTGTTAATGGGAGTACGTCTTCTAAAATACCTTTATGGAAATCGTACTCACGTTTGAAGTCTTCACCTGTTTTCGTTAACTGCTCATCAAGTGATTTACTATCAACACGAATTCCCATTGATG
+
CCCFFFFFGHHHHJJIJIJJIIJDIJJJJJJGJIJIIJJJJJIIECGEIGJJJIFIJIHHHHHHHFFFFFED=ABBDDDDDDCDDDC@CDDDCDDDC>CCDDDDCBBCCCDCDDDDCCA@ACDEDDEDDECDDDDD@9&(8:>CDDDCDCA
@:89:A0172:1:1:19103:29594 1:N:0:1
NTCAATTGAGTATCCTTTCGCAAGCCCTGCTGTAACTGCTGAAGCAAATGTACACCCGCTTCCATGCGTTTGCTTTGAAGGAATTCGTTCACTTTTAAATTCAATAAACTTTTCTCCATCAAAAAGTAAATCAATTACTTCATTACCTTGA
+
#114422232222222223343342211111111111000000000000000110.-.----.....-,,,,....-----,-,,,,,,,,,,,++++++++++++(++,++++++++,++++(+)+++++++++++++++++++(++++(
@:89:A0172:1:1:19050:29614 1:N:0:1
NCAATATGGGAATTTTGCTTCTCGAACAAGGGGGTGATCCGCTTTTTCTGGAACGAGAATTGTGATTTGAACCCCGCGTTTTCGTGCTTCTAATAATGCATTCATAATTTTTCTTCCAGGAATGAAATATGGTGTACCGATAAAGAGTTCT
+
#14442222222232223333333342221111000..//.----.........,,,,,..---------,,,,,,)))))+,)++++++++++++++++++++++++++++++++(+++++++++,+++++++++++))))+++++++,+
@:89:A0172:1:2:17834:1321 1:N:0:1
TCAAACAGCATGGGCGTTAGATGCTCTCATTTCTTACTATGATAAAGAAACACCAACTATTCGAAAAGGCGTTTCATATTTGCTTGCGAATCCTTATGTGAATGAAAAATATCCTACTGGAACAGGTTTACCTGGTGGGTTTTATATTCGT
+
<@@FFFFFFHHHHIDHGIGGHIJFHIIHJIIGGGIG@DDFHCIGIIGIJJGIBFEIGIIJIJIJJFGHHFEDDBCEEEDEEACDDC?@BDDBCCCCCDDEED>@CCCDDBDDDEDD@CDDCAADCBDCCCC@CDD:9?B&2(2:AA>@B<A
@:89:A0172:1:2:16184:1324 1:N:0:1
TTAAAACCATGTTAATATATTTTTGTATAATTAAGAATTTAATTTACAAGGGGGATTATATATGTTCAAAAAAGTAGCTGCTGATGTTTTAGGGTTAAGTGATGTAGGTTCTGTCATTACACCGAAAGATTATGACAAGGTCGATGCTGAT
+
?@@FDDDDDHDFHIIIGGGIHIIGGFIIGIIIIIIFEIIIIIGGIIIIGHIGIIHHIIIGIIIIIDGCEGEEFF@CECEECDDD;>>CCCDDDDCBDCAACDEDBACCC@CDDEDDDEEDAAA@BBDDCDDDCD@>>A8?:()0<ABCCD@