[Bioc-sig-seq] large BAM files and large bed files
rene.paradis at genome.ulaval.ca
Fri Sep 16 15:17:39 CEST 2011
I am experiencing a problem regarding the load in memory of bed files of
30 GB. my function read.table unleash the error : Error in unique(x) :
length xxxxxx is too large for hashing.
this is generated by the function MKsetup of the unique.c file. Even by
increasing by 10 000x the value, the error persists. I believe the
function pushes more data in ram, but I am not sure this is the good way
to focus on.
Ultimately, I would like to produce a GenomeData object from either a
BAM file or a bed file.
has someone ever worked with very very big BAM files (about 30 GB)
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