EVA-1665 VCF headers list the contigs in accession order #172
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Of course this is platform dependent, but given that we have some species with lots of contigs (e.g. almost 0.5M for rat or turkey), we can either: - keep the hacky implementation of this commit. - evaluate memory performance of: loading the file into a list, sort the list in memory, write the list. For at least a couple million of 20 bytes strings. If we go for the second option, the changes have to be done in the same place as the current system sort.
jmmut
commented
Oct 1, 2019
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| private void sortContigFile() { | ||
| try { | ||
| Process process = Runtime.getRuntime().exec(new String[]{"sort", this.output.getAbsolutePath()}); |
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instead of reading sort's standard output, why not using
Suggested change
| Process process = Runtime.getRuntime().exec(new String[]{"sort", this.output.getAbsolutePath()}); | |
| String[] command = {"sort", "-o", this.output.getAbsolutePath(), this.output.getAbsolutePath()}; | |
| Process process = Runtime.getRuntime().exec(command); |
?
it was my bad to use sort without arguments but this is what I had in mind from the beginning.
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Of course this is platform dependent, but given that we have some
species with lots of contigs (e.g. almost 0.5M for rat or turkey),
we can either:
a list, sort the list in memory, write the list. For at least a
couple million of 20 bytes strings.
If we go for the second option, the changes have to be done in the
same place as the current system sort.