Closed jvlasblom closed 10 years ago
Can you confirm that this library can handle very large VCF files ? E.g. 1-5GB
On Mon, Feb 10, 2014 at 3:57 PM, jvlasblom notifications@github.com wrote:
All VCFs are sorted with an external sorting library (ExternalSort), should be fixed.
Reply to this email directly or view it on GitHubhttps://github.com/compbio-UofT/medsavant/issues/280#issuecomment-34681349 .
Should be no problem if there's enough disk space, and filesize / EXTERNALSORT_MAX_TMPFILES bytes of memory available.
(EXTERNAL_SORT_MAX_TMPFILES is currently set to 128)
https://code.google.com/p/externalsortinginjava/
On 10/02/14 03:59 PM, mfiume wrote:
Can you confirm that this library can handle very large VCF files ? E.g. 1-5GB
On Mon, Feb 10, 2014 at 3:57 PM, jvlasblom notifications@github.com wrote:
All VCFs are sorted with an external sorting library (ExternalSort), should be fixed.
Reply to this email directly or view it on GitHubhttps://github.com/compbio-UofT/medsavant/issues/280#issuecomment-34681349 .
— Reply to this email directly or view it on GitHub https://github.com/compbio-UofT/medsavant/issues/280#issuecomment-34681629.
Should be fixed. If any VCF fails to import, it should no longer be because of sorting.
All VCFs are sorted with an external sorting library (ExternalSort), should be fixed.