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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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Add clean=TRUE to getSeqLengths() #37

Closed HenrikBengtsson closed 7 years ago

HenrikBengtsson commented 8 years ago

Add argument clean=TRUE to getSeqLengths() for FastaReferenceFile etc. similar to getSeqNames(). Because now we might get:

> head(getSeqNames(fas[[2]]))
[1] "1" "2" "3" "4" "5" "6"

> head(getSeqLengths(fas[[2]]))
1 dna:chromosome chromosome:GRCh37:1:1:249250621:1
                                         249250621
2 dna:chromosome chromosome:GRCh37:2:1:243199373:1
                                         243199373
3 dna:chromosome chromosome:GRCh37:3:1:198022430:1
                                         198022430
4 dna:chromosome chromosome:GRCh37:4:1:191154276:1
                                         191154276
5 dna:chromosome chromosome:GRCh37:5:1:180915260:1
                                         180915260
6 dna:chromosome chromosome:GRCh37:6:1:171115067:1
                                         171115067