WISH: FastqDataFile and BamDataFile report on read lengths

HenrikBengtsson / aroma.seq

🔬 R package: aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

https://github.com/HenrikBengtsson/aroma.seq

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WISH: FastqDataFile and BamDataFile report on read lengths #13

Open HenrikBengtsson opened 9 years ago

HenrikBengtsson commented 9 years ago

It would be convenient if the FastqDataFile and/or BamDataFile classes could report on read length. The question is, are all reads always of the same lengths? If not, then one needs to report on the first (few) reads.

HenrikBengtsson commented 9 years ago

So, FastqDataFile already does this, e.g.

> fq
FastqDataFile:
Name: reads_2
Tags:
Full name: reads_2
Pathname: fastqData/TopHat-example/LambdaPhage/reads_2.fq
File size: 17.29 kB (17703 bytes)
RAM: 0.00 MB
Is paired: FALSE
Number of sequences: 100
Common width of sequences: 75

However, one need to make sure to "force" parsing of the file first (e.g. using nbrOfSeqs(fq)), otherwise all values are NA.