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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
The text was updated successfully, but these errors were encountered:
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 aaaaaa
aaa`aaaa_^a```]][Z[DY^XYV^_Yksdsada
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
The text was updated successfully, but these errors were encountered: