Fix failure in tandem when trim bypassed

[zwets]

With --bypass-trim a failure occurs in utilities.fastq_to_fasta(), due to generation of an invalid fasta file name in run.tandem().

The offending statement is:

input_fastq.replace(os.path.splitext(input_fastq)[-1],config.fasta_file_extension)

When input_fastq has no extension (as is the case when --bypass-trim), then this evaluates to input_fastq.replace("",".fasta"), which results in .fasta being inserted at every position in input_fastq. This generates file names such as .fasta/.fastap.fastaa.fastat.fastah.fasta/.fastaf.fastai.fastal.fastae.fasta.

This patch fixes the issue simply by appending ".fasta" to input_fastq.

Note: PR #21 fixes an independent issue which prevents the offending filename from being shown in the error message.

[ginolhac]

thanks a lot! This PR should be merged. current 0.12.0 is failing without this fix