Lowercase option not working

[Citteny]

Hi, First i would like to thank you for this awesome tool! I recently started using fastq files with mixed uppercase and lowercase. I'm using fqtools 2.3 2019-05-08 (zlib 1.2.8; htslib 1.8).

A test file I created named test_lowercase.fastq which contains:

@A00740:65:HNY73DSXX:3:1103:7925:25645 1:N:0:GTCCTTGA+TAATCTTA
agccatgcactctgtaatgaagagttcacAATCTTCAACAGAGTAGATATTTCAAGAAGTCAACTGATAGATGAATTGGCAGATAAATTTAACCGGCTTCTTGAAGATTTTCTGCAAGAGGTATATATTATAACTATTACAAGTATTTTGTCAGTTgagcccctctactgcaggaa
+
FFFFFFFFFFFFFFFFFFFF:FFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFFFFFFFFFFFFFFFFFFFFFFF

The command I'm using: fqtools -l count test_lowercase.fastq And the error is: ERROR [line 2]: invalid sequence character (a)

I also tried: fqtools -l -F count test_lowercase.fastq Which outputs a different error:

ERROR: unknown command: "test_lowercase.fastq"
usage: fqtools [-hvdramuli] [-b BUFSIZE] [-B BUFSIZE] [-q QUALTYPE] [-f FORMAT] [-F FORMAT] COMMAND [...] [FILE] [FILE]

I must say I first used an older version which I already had fqtools 2.1 2016-10-04 (zlib 1.2.7; htslib 1.8) had the same results. Decided to clone the repository again.

Am I using the command in the wrong way or is it a bug?

Thank you

[alastair-droop]

Good afternoon.

Using your test example (in a file "test.fastq", I find the command fqtools -dul count test.fastq works. The global options -dul (DNA bases; lowercase and uppercase) need to come before the command.

I hope this works for you!