Bug in getSummaryFile due to bug in readr

[alartin]

Hi,
There is a bug in readr read_tsv and it only parses partial bacteria assembly_summary file. For example, there is over 80,000 rows and only 40,000 + rows loaded due to the quote. But read_tsv lacks of qoute option and it can be fixed by read_delim which you can set quote option.

[HajkD]

Hi Xin,

thank you so much for pointing this out to me!
I wasn't aware of this readr package bug.

I will replace read_tsv by read_delim today and come back to you.

Many thanks!

[HajkD]

Hi Xin,

I just fixed the problem.

Please find all news here: https://github.com/HajkD/biomartr/blob/master/NEWS.md#bug-fixes

I now fixed all affected functions: getSummaryFile(), getKingdomAssemblySummary(), getMetaGenomeSummary(), getENSEMBL.Seq() and getENSEMBLGENOMES.Seq().

I will submit the new version of biomartr to CRAN in one or two weeks. But you can already install via devtools from github.

Again, many thanks for your help. I appreciate it a lot!