Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

invalid fastq file not being detected #10

Open
vcepeda opened this issue Dec 8, 2014 · 0 comments
Open

invalid fastq file not being detected #10

vcepeda opened this issue Dec 8, 2014 · 0 comments

Comments

@vcepeda
Copy link

vcepeda commented Dec 8, 2014

It seems like Lighter just checks if the first character of the file is '@' to consider it valid.
For example, this input file (test.fq) was considered correct:
@iris:7:1:17:394#0/1
GTCAGGACAAGAAAGACAANTCCAATTNACATTATG
IRIS:7:1:17:394#0/1
aaabaa]baaaaa_aab]D^^baYDW]abaa^
IRIS:7:1:17:800#0/1
GGAAACACTACTTAGGCTTATAAGATCNGGTTGCGG
IRIS:7:1:17:800#0/1
ababbaaabaaaaa]ba]aaaaYD_aXT IRIS:7:1:17:1757#0/1 TTTTCTCGACGATTTCCACTCCTGGTCNACGAATCC IRIS:7:1:17:1757#0/1 aaaaaaaaa`aaaa_^a```]][Z[DY^XYV^_Y
ksdsada
dada
e
e
5

output:
./lighter -r test.fq -k 17 5000000 0.1 -t 10
[2014-12-08 11:35:35] =============Start====================
[2014-12-08 11:35:35] Bad quality threshold is "T"
[2014-12-08 11:35:36] Finish sampling kmers
[2014-12-08 11:35:36] Bloom filter A's error rate: 0.000000
[2014-12-08 11:35:36] Finish storing trusted kmers
[2014-12-08 11:35:36] Finish error correction
Processed 5 reads:
0 are error-free
Corrected 0 bases(0.000000 corrections for reads with errors)
Trimmed 0 reads with average trimmed bases 0.000000
Discard 0 reads

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant