Hi,

using:

flagL <- scanBamFlag(isDuplicate=FALSE, isNotPassingQualityControls=FALSE)
ParamL <- ScanBamParam(flag = flagL, what="seq")
BAM <- readGAlignmentPairs(file.bam,use.names = T, param = ParamL)

I don't get anything in mcols(BAM)$seq ... there is no metadata whatsoever. But If I use readGAlignments() function It works fine.

Does readGAlignmentPairs() support importing of actual sequences? I don't get any error, there is just nothing read in. If it does, how can I make it work, if it doesn't what is the suggested workaround?

Thank you!
Lovro

Check out the individual elements, e.g., for

library(pasillaBamSubset)
bam <- untreated3_chr4() 

I have

> gap = readGAlignmentPairs(bam, param=ScanBamParam(what="seq"))
> first(gap)
GAlignments object with 75409 alignments and 1 metadata column:
          seqnames strand       cigar    qwidth     start       end     width
             <Rle>  <Rle> <character> <integer> <integer> <integer> <integer>
      [1]     chr4      +         37M        37       169       205        37
      [2]     chr4      +         37M        37       943       979        37
      [3]     chr4      +         37M        37       944       980        37
      [4]     chr4      +         37M        37       946       982        37
      [5]     chr4      +         37M        37       966      1002        37
      ...      ...    ...         ...       ...       ...       ...       ...
  [75405]     chr4      -         37M        37   1348209   1348245        37
  [75406]     chr4      -         37M        37   1348211   1348247        37
  [75407]     chr4      +         37M        37   1348217   1348253        37
  [75408]     chr4      +         37M        37   1349196   1349232        37
  [75409]     chr4      +         37M        37   1349708   1349744        37
              njunc |                     seq
          <integer> |          <DNAStringSet>
      [1]         0 | CCGTTTCTGA...GTACCTGCCT
      [2]         0 | GCCCCTTTCC...AGCTCATTTC
      [3]         0 | CCCCTTTCCT...GCTCATTTCC
      [4]         0 | CCTTTCCTGG...TCATTTCCCG
      [5]         0 | CGCTAGCTCA...GTGTCCCGGG
      ...       ... .                     ...
  [75405]         0 | GCAGTACTCC...AAAGGGTCTG
  [75406]         0 | AGTACTCACG...AGGGTCTGGC
  [75407]         0 | CCCGCATTTA...TGGCAACAAG
  [75408]         0 | GGCATTTATT...TAAAAATATA
  [75409]         0 | GGCATTTATT...TAAAAATATA
  -------
  seqinfo: 8 sequences from an unspecified genome

Hi,

I get the same.

Looks like I had the data read in all along, but they are only displayed when functions first() and last() are used instead of printing the whole object.

Thank you very much!

Lovro