metaSNV merge requestshttps://git.embl.de/rmuench/metaSNP/-/merge_requests2017-03-17T15:41:45Zhttps://git.embl.de/rmuench/metaSNP/-/merge_requests/10Merge branch 'master' into 'master'2017-03-17T15:41:45ZRobin Erich MuenchMerge branch 'master' into 'master'Update script to make SNP caller commands: add command line options to pass to caller & mpileup.
See merge request !5Update script to make SNP caller commands: add command line options to pass to caller & mpileup.
See merge request !5https://git.embl.de/rmuench/metaSNP/-/merge_requests/9Revert "Merge branch 'master' into 'master'"2017-03-17T15:16:25ZRobin Erich MuenchRevert "Merge branch 'master' into 'master'"This reverts merge request !5This reverts merge request !5https://git.embl.de/rmuench/metaSNP/-/merge_requests/8Refactor to make code simpler2017-03-15T20:22:03ZLuis Pedro Coelholuis.pedro.coelho@embl.deRefactor to make code simplerThis code has fewer repetitions and is more readable.
Again, please review & test. This one is just cosmetics, but still, it looks better and should be faster.This code has fewer repetitions and is more readable.
Again, please review & test. This one is just cosmetics, but still, it looks better and should be faster.https://git.embl.de/rmuench/metaSNP/-/merge_requests/7Probable fix for probable issue2017-03-17T13:37:40ZLuis Pedro Coelholuis.pedro.coelho@embl.deProbable fix for probable issueI believe the previous code was wrong in that the weights were not used
correctly and the splits were arbitrary.
Please test review as I don't have an easy way of testing this atm.I believe the previous code was wrong in that the weights were not used
correctly and the splits were arbitrary.
Please test review as I don't have an easy way of testing this atm.https://git.embl.de/rmuench/metaSNP/-/merge_requests/6DOC Spell check comments2017-03-15T18:22:00ZLuis Pedro Coelholuis.pedro.coelho@embl.deDOC Spell check commentshttps://git.embl.de/rmuench/metaSNP/-/merge_requests/5Update script to make SNP caller commands: add command line options to pass t...2017-03-17T15:17:36ZThomas Sebastian Schmidtsebastian.schmidt@embl.deUpdate script to make SNP caller commands: add command line options to pass to caller & mpileup.This commit allows to pass command line options through the bash script metaSNP_SNP directly to the caller and to mpileup.
The following options are introduced:
- minimum coverage (“-c”, default 4)
- minimum threhold (“-t”, default 4)
-...This commit allows to pass command line options through the bash script metaSNP_SNP directly to the caller and to mpileup.
The following options are introduced:
- minimum coverage (“-c”, default 4)
- minimum threhold (“-t”, default 4)
- minimum frequency (“-p”, default 0.01)
- maximum depth per position and sample for mpileup (“-d”, mirroring mpileup -d option, default 20,000)
- rename debugging option from “-d” to “-D”https://git.embl.de/rmuench/metaSNP/-/merge_requests/4Make thresholds command line options instead of hard coded2017-01-23T14:14:57ZLuis Pedro Coelholuis.pedro.coelho@embl.deMake thresholds command line options instead of hard codedAlso:
- Fix a crash when -i option is missing
- Add Makefile dependencyAlso:
- Fix a crash when -i option is missing
- Add Makefile dependencyhttps://git.embl.de/rmuench/metaSNP/-/merge_requests/3Remove unused function2017-01-23T13:35:24ZLuis Pedro Coelholuis.pedro.coelho@embl.deRemove unused functionhttps://git.embl.de/rmuench/metaSNP/-/merge_requests/2Improve documentation2017-01-21T09:02:29ZLuis Pedro Coelholuis.pedro.coelho@embl.deImprove documentationhttps://git.embl.de/rmuench/metaSNP/-/merge_requests/1Make building more standard: just run make2016-08-17T16:52:33ZLuis Pedro Coelholuis.pedro.coelho@embl.deMake building more standard: just run make