Include input read filenames to log

[nathanhaigh]

I've run ngmlr on multiple files and sent the log info to file. Looking at the logs, it's not easy to determine which belongs to which since the output only shows info about the reference file used and not the reads used:

ngmlr 0.2.6 (build: Jul  6 2017 11:34:03, start: 2017-07-07.13:41:09)
Contact: [email protected]
Wrinting output (SAM) to stdout
Reading encoded reference from reference/my_reference.fasta.gz-enc.2.ngm
Reading 4833 Mbp from disk took 10.99s
Reading RefTable from reference/my_reference.fasta.gz-ht-13-2.2.ngm
Reading from disk took 23.77s
Mapping reads...
Processed: 197 (0.63), R/S: 98.50, RL: 24514, Time: 13.12 6.00 28.75, Align: 0.96, 519, 0.79

[philres]

Thanks for the feedback! Starting from the next release ngmlr will print the read file name as well.

Philipp