search

HenrikBengtsson / aroma.seq

🔬 R package: aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework
https://github.com/HenrikBengtsson/aroma.seq
0 stars 1 forks source link

BamDataFile should report on whether there are paired end reads or not #16

Open HenrikBengtsson opened 9 years ago

HenrikBengtsson commented 9 years ago

BamDataFile should report on whether there are paired end reads or not in the file. Maybe there could also be both SE and PE reads?

HenrikBengtsson commented 9 years ago

As a start:

> getFlagStat(bams[[1]])
                                     description passed failed
1   in total (QC-passed reads + QC-failed reads)    100      0
2                                     duplicates      0      0
3                           mapped (0.00%:-nan%)      0      0
4                           paired in sequencing      0      0
5                                          read1      0      0
6                                          read2      0      0
7                  properly paired (-nan%:-nan%)      0      0
8                    with itself and mate mapped      0      0
9                       singletons (-nan%:-nan%)      0      0
10           with mate mapped to a different chr      0      0
11 with mate mapped to a different chr (mapQ>=5)      0      0