search

amplab / snap

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
https://www.microsoft.com/en-us/research/project/snap/
Apache License 2.0
287 stars 66 forks source link

Error message about long reads needs to be updated #88

Open taltman opened 7 years ago

taltman commented 7 years ago

When I erroneously try to use standard SNAP to align reads of length >400bp, I get the following error message:

BaseAligner:: got too big read (510 > 400)                                                                                                                                                                                                                                                       
Increase MAX_READ_LENGTH at the beginning of Read.h and recompile

But when poking around the SNAP Makefile, it seems that the proper fix is to build snapxl:

make snapxl

So my request is that the error message would print the more helpful make command suggestion, rather than talk about editing source code (that not everyone will be comfortable with).

I would also like to know why the arbitrary distinction is needed; can't SNAP have the smarts to deal with reads of either length at run-time?