From: Michael R. Crusoe <michael.crusoe@gmail.com>
Subject: fix spelling typos
--- vg.orig/src/unittest/genotypekit.cpp
+++ vg/src/unittest/genotypekit.cpp
@@ -431,7 +431,7 @@
   REQUIRE(found_trav_2);
 }
 
-TEST_CASE("SnarlFinder can differntiate ultrabubbles from snarls", "[genotype]") {
+TEST_CASE("SnarlFinder can differentiate ultrabubbles from snarls", "[genotype]") {
 
   SECTION("Directed cycle does not count as ultrabubble") {
     
--- vg.orig/src/unittest/aligner.cpp
+++ vg/src/unittest/aligner.cpp
@@ -123,7 +123,7 @@
     aligner_1.align(aln1, graph, true, false);
     aligner_2.align(aln2, graph, true, false);
     
-    SECTION("left end is detatched without bonus") {
+    SECTION("left end is detached without bonus") {
         REQUIRE(aln1.path().mapping_size() == 1);
         REQUIRE(aln1.path().mapping(0).position().node_id() == n0->id());
         REQUIRE(aln1.path().mapping(0).position().offset() == 2);
@@ -158,7 +158,7 @@
     aligner_1.align(aln1, graph, true, false);
     aligner_2.align(aln2, graph, true, false);
     
-    SECTION("right end is detatched without bonus") {
+    SECTION("right end is detached without bonus") {
         REQUIRE(aln1.path().mapping_size() == 1);
         REQUIRE(aln1.path().mapping(0).position().node_id() == n0->id());
         REQUIRE(aln1.path().mapping(0).position().offset() == 0);
--- vg.orig/src/subcommand/mod_main.cpp
+++ vg/src/subcommand/mod_main.cpp
@@ -52,7 +52,7 @@
          << "                            edges from old to new copies to convert the graph into a DAG" << endl
          << "                            until the shortest path through each SCC is N bases long" << endl
          << "    -L, --dagify-len-max N  stop a dagification step if the unrolling component has this much sequence" << endl
-         << "    -f, --unfold N          represent inversions accesible up to N from the forward" << endl
+         << "    -f, --unfold N          represent inversions accessible up to N from the forward" << endl
          << "                            component of the graph" << endl
          << "    -O, --orient-forward    orient the nodes in the graph forward" << endl
          << "    -N, --remove-non-path   keep only nodes and edges which are part of paths" << endl
--- vg.orig/src/subcommand/find_main.cpp
+++ vg/src/subcommand/find_main.cpp
@@ -51,7 +51,7 @@
          << "sequences:" << endl
          << "    -g, --gcsa FILE        use this GCSA2 index of the sequence space of the graph" << endl
          << "    -z, --kmer-size N      split up --sequence into kmers of size N" << endl
-         << "    -j, --kmer-stride N    step distance between succesive kmers in sequence (default 1)" << endl
+         << "    -j, --kmer-stride N    step distance between successive kmers in sequence (default 1)" << endl
          << "    -S, --sequence STR     search for sequence STR using --kmer-size kmers" << endl
          << "    -M, --mems STR         describe the super-maximal exact matches of the STR (gcsa2) in JSON" << endl
          << "    -B, --reseed-length N  find non-super-maximal MEMs inside SMEMs of length at least N" << endl
--- vg.orig/src/subcommand/genotype_main.cpp
+++ vg/src/subcommand/genotype_main.cpp
@@ -34,7 +34,7 @@
          << "    -A, --no_indel_realign  disable indel realignment" << endl
          << "    -d, --het_prior_denom   denominator for prior probability of heterozygousness" << endl
          << "    -P, --min_per_strand    min unique reads per strand for a called allele to accept a call" << endl
-         << "    -E, --no_embed          dont embed gam edits into grpah" << endl
+         << "    -E, --no_embed          don't embed gam edits into graph" << endl
          << "    -T, --traversal         traversal finder to use {reads, exhaustive, representative, adaptive} (adaptive)" << endl
          << "    -p, --progress          show progress" << endl
          << "    -t, --threads N         number of threads to use" << endl;
--- vg.orig/src/subcommand/gamcompare_main.cpp
+++ vg/src/subcommand/gamcompare_main.cpp
@@ -23,7 +23,7 @@
          << endl
          << "options:" << endl
          << "    -r, --range N            distance within which to consider reads correct" << endl
-         << "    -T, --tsv                output TSV (correct, mq, aligner, read) comaptible with plot-qq.R instead of GAM" << endl
+         << "    -T, --tsv                output TSV (correct, mq, aligner, read) compatible with plot-qq.R instead of GAM" << endl
          << "    -a, --aligner            aligner name for TSV output [\"vg\"]" << endl
          << "    -t, --threads N          number of threads to use" << endl;
 }
--- vg.orig/src/subcommand/view_main.cpp
+++ vg/src/subcommand/view_main.cpp
@@ -76,7 +76,7 @@
          << "    -X, --fastq-out            output fastq (input defaults to GAM)" << endl
          << "    -i, --interleaved          fastq is interleaved paired-ended" << endl
 
-         << "    -L, --pileup               ouput VG Pileup format" << endl
+         << "    -L, --pileup               output VG Pileup format" << endl
          << "    -l, --pileup-in            input VG Pileup format" << endl
 
          << "    -R, --snarl-in             input VG Snarl format" << endl
--- vg.orig/src/sampler.cpp
+++ vg/src/sampler.cpp
@@ -630,7 +630,7 @@
     }
     
     if (!source_paths.empty() && !transcript_expressions.empty()) {
-        cerr << "error:[NGSSimulator] cannot simultaneously limit sampling to paths and match an expresssion profile" << endl;
+        cerr << "error:[NGSSimulator] cannot simultaneously limit sampling to paths and match an expression profile" << endl;
         exit(1);
     }
     
--- vg.orig/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc
+++ vg/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc
@@ -627,7 +627,7 @@
        ||
        interactions_settings_doubled /*settings were restored from model file to file_options and overriden by params from command line*/)
   {
-    arg.trace_message << "WARNING: model file has set of {-q, --cubic, --interactions} settings stored, but they'll be OVERRIDEN by set of {-q, --cubic, --interactions} settings from command line." << endl;
+    arg.trace_message << "WARNING: model file has set of {-q, --cubic, --interactions} settings stored, but they'll be OVERRIDDEN by set of {-q, --cubic, --interactions} settings from command line." << endl;
 
     // in case arrays were already filled in with values from old model file - reset them
     if (!arg.all->pairs.empty()) arg.all->pairs.clear();
--- vg.orig/deps/vowpal_wabbit/vowpalwabbit/global_data.h
+++ vg/deps/vowpal_wabbit/vowpalwabbit/global_data.h
@@ -160,7 +160,7 @@
       uint64_t hash = uniform_hash((unsigned char*)l.begin, l.end-l.begin, 378401);
       uint64_t id = name2id.get(l, hash);
       if (id != 0) // TODO: memory leak: char* temp
-        THROW("error: label dictionary initialized with multiple occurances of: " << l);
+        THROW("error: label dictionary initialized with multiple occurrences of: " << l);
       size_t len = l.end - l.begin;
       substring l_copy = { calloc_or_throw<char>(len), nullptr };
       memcpy(l_copy.begin, l.begin, len * sizeof(char));
--- vg.orig/src/index.cpp
+++ vg/src/index.cpp
@@ -2140,7 +2140,7 @@
             string kmer;
             parse_kmer(key, value, kmer, id, pos);
 
-            // only visit first kmer when multiple occurances with dif. ids in a row
+            // only visit first kmer when multiple occurrences with dif. ids in a row
             if (kmer != prev_kmer) {
 
                 string remk = reverse_complement(kmer);
--- vg.orig/deps/vowpal_wabbit/vowpalwabbit/cost_sensitive.cc
+++ vg/deps/vowpal_wabbit/vowpalwabbit/cost_sensitive.cc
@@ -23,7 +23,7 @@
       THROW("error NaN value for: " << name[0]);
     break;
   default:
-    cerr << "example with a wierd name.  What is '";
+    cerr << "example with a weird name.  What is '";
     cerr.write(s.begin, s.end - s.begin);
     cerr << "'?\n";
   }
--- vg.orig/src/subcommand/chunk_main.cpp
+++ vg/src/subcommand/chunk_main.cpp
@@ -74,7 +74,7 @@
          << "    -T, --trace              trace haplotype threads in chunks (and only expand forward from input coordinates)." << endl
          << "                             Produces a .annotate.txt file with haplotype frequencies for each chunk." << endl 
          << "    -f, --fully-contained    only return GAM alignments that are fully contained within chunk" << endl
-         << "    -O, --output-fmt         Specifiy output format (vg, pg, hg).  [VG]" << endl
+         << "    -O, --output-fmt         Specify output format (vg, pg, hg).  [VG]" << endl
          << "    -t, --threads N          for tasks that can be done in parallel, use this many threads [1]" << endl
          << "    -h, --help" << endl;
 }
@@ -301,7 +301,7 @@
     // check the output format
     std::transform(output_format.begin(), output_format.end(), output_format.begin(), ::tolower);
     if (!vg::io::valid_output_format(output_format)) {
-        cerr << "error[vg chunk]: invalid ouput format" << endl;
+        cerr << "error[vg chunk]: invalid output format" << endl;
         return 1;
     }
 
