diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnAssembler.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnAssembler.java index 5ce65e13f..0e1d49d81 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnAssembler.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnAssembler.java @@ -81,7 +81,7 @@ public class DeBruijnAssembler extends LocalAssemblyEngine { private static final int KMER_OVERLAP = 5; // the additional size of a valid chunk of sequence, used to string together k-mers - // TODO -- this number is very low, and limits our ability to explore low-frequnecy variants. It should + // TODO -- this number is very low, and limits our ability to explore low-frequency variants. It should // TODO -- be increased to a large number of eliminated altogether when moving to the bubble caller where // TODO -- we are no longer considering a combinatorial number of haplotypes as the number of bubbles increases private static final int NUM_BEST_PATHS_PER_KMER_GRAPH = 25; @@ -187,10 +187,10 @@ public class DeBruijnAssembler extends LocalAssemblyEngine { // TODO -- we need to come up with a consistent pruning algorithm. The current pruning algorithm // TODO -- works well but it doesn't differentiate between an isolated chain that doesn't connect - // TODO -- to anything from one that's actuall has good support along the chain but just happens + // TODO -- to anything from one that's actually has good support along the chain but just happens // TODO -- to have a connection in the middle that has weight of < pruneFactor. Ultimately // TODO -- the pruning algorithm really should be an error correction algorithm that knows more - // TODO -- about the structure of the data and can differeniate between an infrequent path but + // TODO -- about the structure of the data and can differentiate between an infrequent path but // TODO -- without evidence against it (such as occurs when a region is hard to get any reads through) // TODO -- from a error with lots of weight going along another similar path // the very first thing we need to do is zip up the graph, or pruneGraph will be too aggressive @@ -216,7 +216,7 @@ public class DeBruijnAssembler extends LocalAssemblyEngine { seqGraph.removePathsNotConnectedToRef(); seqGraph.simplifyGraph(); if ( seqGraph.vertexSet().size() == 1 ) { - // we've prefectly assembled into a single reference haplotype, add a empty seq vertex to stop + // we've perfectly assembled into a single reference haplotype, add a empty seq vertex to stop // the code from blowing up. // TODO -- ref properties should really be on the vertices, not the graph itself final SeqVertex complete = seqGraph.vertexSet().iterator().next(); diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java index a17e25f41..6ea543f25 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java @@ -308,7 +308,7 @@ public class HaplotypeCaller extends ActiveRegionWalker implem protected boolean useLowQualityBasesForAssembly = false; @Hidden - @Argument(fullName="dontTrimActiveRegions", shortName="donTrimActiveRegions", doc="If specified, we will not trim down the active region from the full region (active + extension) to just the active interval for genotyping", required = false) + @Argument(fullName="dontTrimActiveRegions", shortName="dontTrimActiveRegions", doc="If specified, we will not trim down the active region from the full region (active + extension) to just the active interval for genotyping", required = false) protected boolean dontTrimActiveRegions = false; @Hidden diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java index bee695e2a..824ef1f6e 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java @@ -173,7 +173,7 @@ public class VariantRecalibrator extends RodWalker