SV/Add Makefile and additional features to Hap-IBD #1
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Add an option that allows the user to restrict comparisons to only the identifiers specified in a text file.
svohr
changed the title
svohr
commented
Nov 20, 2024
| @@ -403,6 +403,8 @@ private static char flipBase(char c) { | |||
| case 'G' : return 'C'; | |||
| case 'T' : return 'A'; | |||
| case 'N' : return 'N'; | |||
| case 'I' : return 'I'; | |||
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Insertions and deletions are the same on both strands.
svohr
commented
Nov 20, 2024
| Set<String> exclude = Utilities.idSet(excludeSamplesFile); | ||
| return Filter.excludeFilter(exclude); | ||
| } | ||
| else if (includeSamplesFile!=null) { | ||
| Set<String> include = Utilities.idSet(includeSamplesFile); | ||
| return Filter.includeFilter(include); |
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Conveniently, the Filter class already has an includeFilter defined.
svohr
commented
Nov 20, 2024
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| // algorithm parameters | ||
| min_mac = Validate.intArg("min-mac", argsMap, false, DEF_MIN_MAC, 1, IMAX); | ||
| min_mac = Validate.intArg("min-mac", argsMap, false, DEF_MIN_MAC, 0, IMAX); |
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min-mac is only used here and if it set to 0 the filtering step is skipped, the same as the case when all markers meet the min-mac requirement.
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This PR adds a Makefile and basic additional features to Hap-IBD. The Makefile makes it easier to rebuild the jar from source. I removed the jar indexing step because it is deprecated.
Additional Features:
IandDas markers for IBD detection. Without this feature, Hap-IBD will throw an exception if it encounters these variants.includesamplesoption similar to theexcludesamplesoption already provided in Hap-IBD but works by excluding all samples that are NOT included in theincludesamplesfile.min-mac=0. This change allows for the same markers to be used for independent runs with different sets of individuals.