FASTQ renaming through samples sheets is broken

[serine]

A sample sheet like this

old_prefix    new_prefix
1       wt_cond1_rep1
5       wt_cond1_rep2
2       wt_cond2_rep1
10      wt_cond2_rep2
7       mt_cond1_rep1
11      mt_cond1_rep2
9       mt_cond2_rep1
12      mt_cond2_rep2

will append samples 1,10,11 and 12 into single sample, because of this line, because all of those five different files start with 1.

I need to think about this problem, but I reckon I need to somehow check/assert that values of samplesMap are all of the same length. and/or somehow check that sample that has been assigned to a different key doesn't get repeated/re-assigned multiple times. Something like "seen" list. Before you put another fastq file into samplesMap check that it hasn't been "seen" and if it hasn't append into samplesMap and if it has raise an error? I guess.

So if anyone want to send a patch through will appreciate this. Otherwise some what lowerish priority, but should fix it this in the next couple of month.

[serine]

As per the commit this issue should be fixed now