search

itmat / rum

RNA-Seq Unified Mapper
http://cbil.upenn.edu/RUM
MIT License
26 stars 4 forks source link

RUM mistakenly flagging some fastq inpu as variable length #148

Closed mdelaurentis closed 11 years ago

mdelaurentis commented 11 years ago

nmanik reports:

Even though my fastq.gz files contain only same-length reads (100bp, paired-end reads), RUM checks the files and thinks they're variable length reads which leads to a lot of other downstream problems.

When I dig in, I find that this only happens for files that've >50k lines, and a quick fix could be the following:

diff --recursive RUM-modified/lib/RUM/Platform/Local.pm RUM-Pipeline-v2.0.3_01/lib/RUM/Platform/Local.pm

220c220
<            ++$len < 50000) { 
---
           $len++ < 50000) {

This makes sure reads_temp.fa has 50,000 instead of 50,001 lines, and hence multiple of 4 fastq files (still testing it out and not sure if this will fix all issues with variable-length checks).