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Minor spelling fixes #44

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Minor spelling fixes #44

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f25eeed
Correct spelling of Hardy-Weinberg.
cbrueffer Aug 6, 2018
786c25c
Fix a few more typos in messages and variable names.
cbrueffer Aug 6, 2018
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8 changes: 4 additions & 4 deletions src/main/java/org/snpsift/SnpSift.java
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Original file line number Diff line number Diff line change
Expand Up @@ -336,7 +336,7 @@ protected boolean databaseDownload() {
// Download tabix index?
if (dbTabix) {
String indexUrl = config.getDatabaseRepository(dbType) + ".tbi";
Timer.showStdErr("Downlading index from " + indexUrl);
Timer.showStdErr("Downloading index from " + indexUrl);
download = new Download();
download.setVerbose(verbose);
download.setDebug(debug);
Expand All @@ -358,8 +358,8 @@ protected String databaseFind() {

// Still empty: Something is wrong!
if (dbFileName == null || dbFileName.isEmpty()) {
String confgiKey = config.getDatabaseLocalKey(dbType);
fatalError("Database file name not found. Missing '" + confgiKey + "' entry in SnpEff's config file?");
String configKey = config.getDatabaseLocalKey(dbType);
fatalError("Database file name not found. Missing '" + configKey + "' entry in SnpEff's config file?");
}
}

Expand Down Expand Up @@ -719,7 +719,7 @@ public void usage(String msg) {
+ "\n\tgt : Add Genotype to INFO fields and remove genotype fields when possible." //
+ "\n\tgtfilter : Filter genotype using arbitrary expressions." //
+ "\n\tgwasCat : Annotate using GWAS catalog" //
+ "\n\thwe : Calculate Hardy-Weimberg parameters and perform a godness of fit test." //
+ "\n\thwe : Calculate Hardy-Weinberg parameters and perform a goodness of fit test." //
+ "\n\tintersect : Intersect intervals (genomic regions)." //
+ "\n\tintervals : Keep variants that intersect with intervals." //
+ "\n\tintIdx : Keep variants that intersect with intervals. Index-based method: Used for large VCF file and a few intervals to retrieve" //
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6 changes: 3 additions & 3 deletions src/main/java/org/snpsift/hwe/VcfHwe.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,11 +6,11 @@
import org.snpeff.vcf.VcfEntry;

/**
* Calculate Hardy-Weimberg equilibrium and goodness of fit.
* Calculate Hardy-Weinberg equilibrium and goodness of fit.
*
* References:
* "Principles of population genetics", Hartl & Clark
* "A Note on Exact test of Hardy Weinbeg Equilibrium", G. Abecasis et. al.
* "A Note on Exact test of Hardy Weinberg Equilibrium", G. Abecasis et. al.
*
* Note: This is only for two alleles in diploid individuals. We should
* extend this to more alleles and N-ploid species.
Expand All @@ -26,7 +26,7 @@ public VcfHwe() {
}

/**
* Calculate Hardy-Weimberg equilibrium and add data to vcfEntry (INFO fields)
* Calculate Hardy-Weinberg equilibrium and add data to vcfEntry (INFO fields)
* @param addInfo : If true, 'HWE' and 'HWEP' INFO tags are added to this entry
*/
public double hwe(VcfEntry vcfEntry, boolean addInfo) {
Expand Down