Yes, it is a sort-merge strategy. dirs and g2g do the same kind of sorting but g2g does the reflection about the diagonal.
It may be helpful to read about genome alignments: http://en.wikipedia.org/wiki/Sequence_alignment Please note the dot-plot: http://en.wikipedia.org/wiki/File:Zinc-finger-dot-plot.png http://en.wikipedia.org/wiki/Dot_plot_%28bioinformatics%29 and tutorial: http://helix.biology.mcmaster.ca/721/outline2/node38.html You can read the pslSort.c code to see how the arguments are used and what happens during g2g. --Hiram ----- Original Message ----- From: "Peng Yu" <[email protected]> To: "Hiram Clawson" <[email protected]> Cc: [email protected] Sent: Tuesday, June 22, 2010 8:18:20 PM GMT -08:00 Tijuana / Baja California Subject: Re: [Genome] According to what does pslSort sort? On Tue, Jun 22, 2010 at 9:49 PM, Hiram Clawson <[email protected]> wrote: > > The procedure is too large to do all in one step. The first step > consolidates the 100s of thousands of files down to perhaps less > than 100 files. Then those ~100 files are put together which is > easy since they are already sorted. So you actually refers to the external sort http://en.wikipedia.org/wiki/External_sorting, right? > If you do not need sorted psl output, then please do not use pslSort. I still don't understand what is the different between dirs and g2g. Would you please let me know what they are. The help page is not clear to me. Also, what does 'diagonal' refers in "reflecting the alignments across the diagonal"? -- Regards, Peng _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
