Merge pull request #4694 from vgteam/helptext-fix

Helptext fix

Author: faithokamoto

src/subcommand/filter_main.cpp

@@ -60,7 +60,7 @@ void help_filter(char** argv) {
          << "  -V, --no-output              print out -v statistics and do not write the GAM" << endl
          << "  -T, --tsv-out FIELD[;FIELD]  write TSV of given fields instead of filtered GAM" << endl
          << "                               See wiki page:" << endl
-         << "                               \"Getting alignment statistics with ‐‐tsv‐out\"" << endl
+         << "                               \"Getting alignment statistics with vg filter\"" << endl
          << "  -q, --min-mapq N             drop alignments with mapping quality < N" << endl
          << "  -E, --repeat-ends N          drop reads with tandem repeat (motif size <= 2N," << endl
          << "                               spanning >= N bases) at either end" << endl
@@ -576,5 +576,5 @@ int main_filter(int argc, char** argv) {
 }
 
 // Register subcommand
-static Subcommand vg_filter("filter", "filter reads", main_filter);
+static Subcommand vg_filter("filter", "filter reads and get statistics by read", main_filter);
 

src/subcommand/gamsort_main.cpp

@@ -206,4 +206,4 @@ int main_gamsort(int argc, char **argv)
     return 0;
 }
 
-static Subcommand vg_gamsort("gamsort", "sort a GAM/GAF file or index a sorted GAM file.", main_gamsort);
+static Subcommand vg_gamsort("gamsort", "sort a GAM/GAF file or index a sorted GAM file", main_gamsort);

src/subcommand/genotype_main.cpp

@@ -366,4 +366,4 @@ int main_genotype(int argc, char** argv) {
 }
 
 
-static Subcommand vg_genotype("genotype", "genotype (or type) graphs, GAMS, and VCFs.", main_genotype);
+static Subcommand vg_genotype("genotype", "genotype (or type) graphs, GAMS, and VCFs", main_genotype);

src/subcommand/giraffe_main.cpp

@@ -2502,4 +2502,4 @@ std::string sample_haplotypes(
 //----------------------------------------------------------------------------
 
 // Register subcommand
-static Subcommand vg_giraffe("giraffe", "fast haplotype-aware short read alignment", PIPELINE, 6, main_giraffe);
+static Subcommand vg_giraffe("giraffe", "fast haplotype-aware read alignment", PIPELINE, 6, main_giraffe);

src/subcommand/surject_main.cpp

@@ -58,7 +58,7 @@ void help_surject(char** argv) {
          << "  -T, --max-tail-len N      only align up to N bases of read tails [10000]" << endl
          << "  -g, --max-graph-scale X   make reads unmapped if alignment target subgraph" << endl
          << "                            size exceeds read length by a factor of X " << endl
-                                         << "(default: " << Surjector::DEFAULT_SUBGRAPH_LIMIT
+         << "                            (default: " << Surjector::DEFAULT_SUBGRAPH_LIMIT
                                          << " or " << Surjector::SPLICED_DEFAULT_SUBGRAPH_LIMIT << " with -S)" << endl
          << "  -P, --prune-low-cplx      prune short/low complexity anchors in realignment" << endl
          << "  -I, --max-slide N         look for offset duplicates of anchors up to N bp" << endl