Correct spelling mistakes

src/main/scala/org/broadinstitute/pilon/BaseSum.scala

@@ -55,8 +55,8 @@ class BaseSum {
   }
 
   def order = {
-    val indicies = List(0,1,2,3).toArray
-    indicies.sortWith({(a,b) => sums(a) > sums(b)})
+    val indices = List(0,1,2,3).toArray
+    indices.sortWith({(a,b) => sums(a) > sums(b)})
   }
 
   def /(divisor : Int) = {

src/main/scala/org/broadinstitute/pilon/GenomeRegion.scala

@@ -50,7 +50,7 @@ class GenomeRegion(val contig: ReferenceSequence, start: Int, stop: Int)
   //var lowCoverage = new Array[Boolean](size)
   //var lowConfidence = new Array[Boolean](size)
 
-  // sumary stats
+  // summary stats
   val badCoverage = new Array[Int](size)
   val clips = new Array[Int](size)
   val copyNumber = new Array[Short](size)

src/main/scala/org/broadinstitute/pilon/PileUp.scala

@@ -228,7 +228,7 @@ class PileUp {
           ("", true)
       } else {
         // new heuristics to call heterozygous indels
-        // the mean pct of reads containing a het indel of a given legnth is something like this:
+        // the mean pct of reads containing a het indel of a given length is something like this:
         val middle = (45 - winStr.length) max 10
         // we define the low het cutoff as half that:
         val low = middle / 2

src/main/scala/org/broadinstitute/pilon/Pilon.scala

@@ -318,13 +318,13 @@ object Pilon {
               for the bam alignments.  At least one of --frags or --jumps must also be given.
            --frags frags.bam
               A bam file consisting of fragment paired-end alignments, aligned to the --genome
-              argument using bwa or bowtie2.  This argument may be specifed more than once.
+              argument using bwa or bowtie2.  This argument may be specified more than once.
            --jumps jumps.bam
               A bam file consisting of jump (mate pair) paired-end alignments, aligned to the
-              --genome argument using bwa or bowtie2.  This argument may be specifed more than once.
+              --genome argument using bwa or bowtie2.  This argument may be specified more than once.
            --unpaired unpaired.bam
               A bam file consisting of unpaired alignments, aligned to the --genome argument 
-              using bwa or bowtie2.  This argument may be specifed more than once.
+              using bwa or bowtie2.  This argument may be specified more than once.
            --bam any.bam
               A bam file of unknown type; Pilon will scan it and attempt to classify it as one
               of the above bam types.
@@ -405,7 +405,7 @@ object Pilon {
               Variants (snps and indels) will only be called if there is coverage of good pairs
               at this depth or more; if this value is >= 1, it is an absolute depth, if it is a
               fraction < 1, then minimum depth is computed by multiplying this value by the mean
-              coverage for the region, with a minumum value of 5 (default 0.1: min depth to call 
+              coverage for the region, with a minimum value of 5 (default 0.1: min depth to call 
               is 10% of mean coverage or 5, whichever is greater).
            --mingap
               Minimum size for unclosed gaps (default 10)