#164 Command line options are incorrectly parsed/ignored

[Anonymous]

bowtie 0.12.7 does not recognize the -q option dependent on where it is given in the command line or the presence of the -fr option. In the following example the forward and reverse reads files are fastq (phred33):

$ bowtie -q "mm9" -fr -1 "1.fastq" -2 "2.fastq"
Time loading reference: 00:00:00
Time loading forward index: 00:00:01
Time loading mirror index: 00:00:00
Error: reads file does not look like a Raw file
Reads file looks like a FASTQ file; please use -q
terminate called after throwing an instance of 'int'
Aborted

The error does not occur If the -fr option is omitted. The following invokation is also successful:

bowtie "mm9" -fr -q -1 "1.fastq" -2 "2.fastq"

Thanks!

Philip

P.S.:
bowtie --version
bowtie version 0.12.7
64-bit
Built on <our server>
Thu Jan 13 13:54:27 CET 2011
Compiler: gcc version 4.1.2 20080704 (Red Hat 4.1.2-46)
Options: -O3 -Wl,--hash-style=both -I/usr/include -I/usr/local/include -I/usr/include -I/usr/local/include
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

[Nobody/Anonymous]

[Ben Langmead]

The --fr option starts with 2 dashes, not 1. This should fix the issue.

Best,
Ben