This flag will skip spectra that don't have any cross-linked candidates, even if they have non-cross-linked candidates. It would be good to print an INFO line indicating how many spectra were skipped due to this flag.
Status: open Milestone: post v2.0 Created: Fri Jun 24, 2016 06:04 PM UTC by William S Noble Last Updated: Fri Jun 24, 2016 06:04 PM UTC Owner: sjoemac
This flag will skip spectra that don't have any cross-linked candidates,
even if they have non-cross-linked candidates. It would be good to print an
INFO line indicating how many spectra were skipped due to this flag.
Should be resolved in rev. 17084. For the report of the number of times the number of spectra are skipped because of this feature, they will always be reported as the number of times candidates=0. This is reported already at the end of search-for-xlinks.
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Sorry, I am having trouble parsing this sentence: "For the report of the number of times the number of spectra are skipped because of this feature, they will always be reported as the number of times candidates=0." Is it possible to have a line such as
"INFO: Skipped 1305 (15.5%) of spectra that have no cross-linked candidates."?
This may be what it reports -- I am running my first search with this option now, but it looks like it will take a few hours to complete.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Would a cross-link candidate include self-loops and/or deadlinks as cross link candidates or just an inter/intra cross peptide?
Last edit: sjoemac 2016-06-28
Just inter/intra.
On Mon, Jun 27, 2016 at 6:25 PM, sjoemac sjoemac@users.sf.net wrote:
Related
Issues: #403
Should be resolved in rev. 17084. For the report of the number of times the number of spectra are skipped because of this feature, they will always be reported as the number of times candidates=0. This is reported already at the end of search-for-xlinks.
Sorry, I am having trouble parsing this sentence: "For the report of the number of times the number of spectra are skipped because of this feature, they will always be reported as the number of times candidates=0." Is it possible to have a line such as
"INFO: Skipped 1305 (15.5%) of spectra that have no cross-linked candidates."?
This may be what it reports -- I am running my first search with this option now, but it looks like it will take a few hours to complete.