Missing reads with `--simplified on`

[maressyl]

Hi,

We are overall very happy with MutScan, but It seems some reads are missed when --simplified is on :

R1.fastq :

@NL500104:785:HCMC2AFX5:1:11303:22509:17003 1:N:0:ACAGTGAC+CAGTGACA
GGAAAGGGAAGGACTGGGAGAGACACAAAGACCAGAGCCAGCCTCAGGGACAAGAGATTCCAGTTTTAGGCCTTT
+
AAAAAEEEE6EEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEE//EEAEEEEEEEEE/EEE/EEEE<EEEEE/<<E

R2.fastq :

@NL500104:785:HCMC2AFX5:1:11303:22509:17003 2:N:0:ACAGTGAC+CAGTGACA
TTCCCTCGTTGAACATGCTGTCAAACCAGGACACTGGCTCCAGCTTGTGTTTCTGTTCTTGACCATCGTCTGGGA
+
AAAAAEEEEEEE6EEEEEEAEAAEEEEEAEEEEEEEEEEEEEEAAEAE<EEEE/EAEEEEE/EEEEEEEEAEE/E

design.conf :

#name, left_seq_of_mutation_point, mutation_seq, right_seq_of_mutation_point, chromosome
rs8017_C, CCAGGACACTGGCTCCAGCTTGTGTTTCTG, C, TCTTGGCCATCGTCTGGGAGTGGACATGCA, chr16
rs8017_T, CCAGGACACTGGCTCCAGCTTGTGTTTCTG, T, TCTTGGCCATCGTCTGGGAGTGGACATGCA, chr16

mutscan --read1 R1.fastq --read2 R2.fastq --support 0 --html mutscan.html --mutation design.conf --simplified on

---------------
rs8017_C CCAGGACACTGGCTCCAGCTTGTGTTTCTG C TCTTGGCCATCGTCTGGGAGTGGACATGCA chr16

---------------
rs8017_T CCAGGACACTGGCTCCAGCTTGTGTTTCTG T TCTTGGCCATCGTCTGGGAGTGGACATGCA chr16

/usr/local/bin/mutscan --read1 R1.fastq --read2 R2.fastq --support 0 --html mutscan.html --mutation design.conf --simplified on
Mutscan v1.14.1, time used: 0 seconds

mutscan --read1 R1.fastq --read2 R2.fastq --support 0 --html mutscan.html --mutation design.conf

---------------
rs8017_C CCAGGACACTGGCTCCAGCTTGTGTTTCTG C TCTTGGCCATCGTCTGGGAGTGGACATGCA chr16

---------------
rs8017_T CCAGGACACTGGCTCCAGCTTGTGTTTCTG T TCTTGGCCATCGTCTGGGAGTGGACATGCA chr16
1, pos: 55, distance: 1, forward
@NL500104:785:HCMC2AFX5:1:11303:22509:17003 2:N:0:ACAGTGAC+CAGTGACA
TTCCCTCGTTGAACATGCTGTCAAA CCAGGACACTGGCTCCAGCTTGTGTTTCTG T TCTTGACCATCGTCTGGGA
+
AAAAAEEEEEEE6EEEEEEAEAAEE EEEAEEEEEEEEEEEEEEAAEAE<EEEE/E A EEEEE/EEEEEEEEAEE/E

/usr/local/bin/mutscan --read1 R1.fastq --read2 R2.fastq --support 0 --html mutscan.html --mutation design.conf
Mutscan v1.14.1, time used: 0 seconds