From f25eeed42ab8d5d69a881a0e2c12fbd56b668891 Mon Sep 17 00:00:00 2001 From: Christian Brueffer Date: Mon, 6 Aug 2018 12:23:45 +0200 Subject: [PATCH 1/2] Correct spelling of Hardy-Weinberg. --- src/main/java/org/snpsift/SnpSift.java | 2 +- src/main/java/org/snpsift/hwe/VcfHwe.java | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/main/java/org/snpsift/SnpSift.java b/src/main/java/org/snpsift/SnpSift.java index 99ac557c..9fe38a5a 100644 --- a/src/main/java/org/snpsift/SnpSift.java +++ b/src/main/java/org/snpsift/SnpSift.java @@ -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 godness 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" // diff --git a/src/main/java/org/snpsift/hwe/VcfHwe.java b/src/main/java/org/snpsift/hwe/VcfHwe.java index 8f7c514c..276aaa85 100644 --- a/src/main/java/org/snpsift/hwe/VcfHwe.java +++ b/src/main/java/org/snpsift/hwe/VcfHwe.java @@ -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. @@ -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) { From 786c25c635041acad6449f0a19f4e97733914808 Mon Sep 17 00:00:00 2001 From: Christian Brueffer Date: Mon, 6 Aug 2018 12:28:29 +0200 Subject: [PATCH 2/2] Fix a few more typos in messages and variable names. --- src/main/java/org/snpsift/SnpSift.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/main/java/org/snpsift/SnpSift.java b/src/main/java/org/snpsift/SnpSift.java index 9fe38a5a..95bec7b3 100644 --- a/src/main/java/org/snpsift/SnpSift.java +++ b/src/main/java/org/snpsift/SnpSift.java @@ -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); @@ -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?"); } } @@ -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-Weinberg 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" //