All paired-end MiSeq reads end up unmatched

[zwets]

Running KneadData against MiSeq paired-end reads results in all reads ending up in *_unmatched_1.fq and *_unmatched_2.fq.

This appears to be a regression introduced in commit ecf589d. In particular, the deletion of these lines:

    if " 1:" in lines[0]:
        lines[0]=lines[0].replace(" 1","").rstrip()+"#0/1\n"
    elif " 2:" in lines[0]:
        lines[0]=lines[0].replace(" 2","").rstrip()+"#0/2\n"

The replace(" 1","") and replace(" 2","") used to strip the Illumina read index, so that reformatted read headers became:

@M01336:233:000000000-AJKD1:1:1101:15356:1498:N:0:15#0/1
@M01336:233:000000000-AJKD1:1:1101:15356:1498:N:0:15#0/2

Since commit ecf589d the headers are rewritten to:

@M01336:233:000000000-AJKD1:1:1101:15356:1498.1:N:0:15#0/1
@M01336:233:000000000-AJKD1:1:1101:15356:1498.2:N:0:15#0/2

and therefore don't match up.

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