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lh3 / seqtk

Toolkit for processing sequences in FASTA/Q formats
MIT License
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seqtk fqchk - gives odd result if given .fa not .fq #87

Open tseemann opened 7 years ago

tseemann commented 7 years ago 

### FASTA ### 

% cat test.fa
>lonely
GATTACA

% seqtk fqchk test.fa
min_len: 2147483647; max_len: 0; avg_len: -nan; 0 distinct quality values
POS     #bases  %A      %C      %G      %T      %N      avgQ    errQ    %low    %high
ALL     0       -nan    -nan    -nan    -nan    -nan    -nan    -0.0    -nan    -nan

### FASTQ ###

% cat test.fq
@loner
AGTC
+
HHHH

% seqtk fqchk test.fq
min_len: 4; max_len: 4; avg_len: 4.00; 1 distinct quality values
POS     #bases  %A      %C      %G      %T      %N      avgQ    errQ    %low    %high
ALL     4       25.0    25.0    25.0    25.0    0.0     39.0    39.0    0.0     100.0
1       1       100.0   0.0     0.0     0.0     0.0     39.0    39.0    0.0     100.0
2       1       0.0     0.0     100.0   0.0     0.0     39.0    39.0    0.0     100.0
3       1       0.0     0.0     0.0     100.0   0.0     39.0    39.0    0.0     100.0
4       1       0.0     100.0   0.0     0.0     0.0     39.0    39.0    0.0     100.0
tseemann commented 6 years ago

I guess i'm going to have to write a pull request.

Except I think it may be addressed in this unreleased commit https://github.com/lh3/seqtk/commit/d210c57d2ffa33da147e50f04f5aaaab1c160c8c