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Last seen 10.5 years ago
Is there a way to sort the records in a GAlignments object by the
QNAME, as this object is created with the readGAlignmentsFromBam
function where the bam file and its corresponding index file must be
sorted by RNAME and POS.
Unless I'm missing something the only way I see how can this be done
is read the bam into a data.table and sort that.
-- output of sessionInfo():
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets
methods base
other attached packages:
[1] doParallel_1.0.3 iterators_1.0.6 foreach_1.4.1
data.table_1.8.10 Rsamtools_1.13.44 Biostrings_2.29.19
GenomicRanges_1.13.45 XVector_0.1.4
[9] IRanges_1.19.38 BiocGenerics_0.7.5
loaded via a namespace (and not attached):
[1] bitops_1.0-6 codetools_0.2-8 stats4_3.0.2 tools_3.0.2
zlibbioc_1.7.0
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