Dear all,

I am using GenomicRanges and Rsamtools a lot for my work, they are extremely
helpful and neat packages to deal with NGS data, thanks a lot for those
people how contribute to all those nice packages in BioC. I just have some
features request for the GappedAlignments, probably it's already there or
it's not a good practice to do it in certain way, please feel free to let me
know.

I like features from both scanBam or readBamGappedAlignments,  just sometime
I need to write my own script trying to combine information from those two
function and make a "general" granges to work with. So I am wondering if
there is any way to do it in a neat way or is there a plan to implement
similiar features?

   - Including more element meta data with GappedAlignments
      - there is "which" in readBamGappedAlignments, can I have some thing
      like "param" or "what" to get more info from bam file and associate them
      with Gapped reads.
      - When doing the coerce from GappedAlignement to GRanges, or call
      granges() on GappedAlignments object, it only return the minimal
      information, "qwidth", "cigar", "ngap" is not included as
elementMetadata.
   - Including more pairing information for pair-end RNA-seq
      - So I could know the mated information with certain gapped reads,
      either plot it as pair-end read or do some computation on it.
      - Setting flags for each entry, so I can filter it out based on the
      flags, something like from scanBamFlag?
      - grglist to transform the data in different way

If I can get a general data structure which combine all those information
and or features together, that would be nice, I realize it's hard  to
combine all information together and make it flexible at the same time ,
 e.g. you need to deal with how to binding element meta data for paired
entry, probably showing seq1/seq2 to indicate which sequence it's belongs
too? how to handle multiple hits?

Right now, I am making my own "giant" GRanges object which including all the
information I want, but that's too specific for my work, that's why I am
wondering if there is any  plan to combine those neat features together and
bring a more flexible data structure.

Thanks!

Tengfei


-- 
Tengfei Yin
MCDB PhD student
1620 Howe Hall, 2274,
Iowa State University
Ames, IA,50011-2274
Homepage: www.tengfei.name

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