From 686a4ee183a8b52739fb5a3b3392a6c5302d4f13 Mon Sep 17 00:00:00 2001
From: edolzhenko <edolzhenko@illumina.com>
Date: Thu, 25 Jan 2018 14:12:34 -0800
Subject: [PATCH] release-2.5.4: Exit normally on help/version request

---
 .clang-format           |  1 +
 common/parameters.cc    |  8 ++++----
 common/parameters.h     | 16 ++++++++++------
 src/expansion_hunter.cc | 30 +++++++++++++++---------------
 4 files changed, 30 insertions(+), 25 deletions(-)
 create mode 100644 .clang-format

diff --git a/.clang-format b/.clang-format
new file mode 100644
index 0000000..f6cb8ad
--- /dev/null
+++ b/.clang-format
@@ -0,0 +1 @@
+BasedOnStyle: Google
diff --git a/common/parameters.cc b/common/parameters.cc
index 0634a86..8e580ed 100644
--- a/common/parameters.cc
+++ b/common/parameters.cc
@@ -36,12 +36,12 @@
 #include <boost/lexical_cast.hpp>
 #include <boost/program_options.hpp>
 
-using boost::lexical_cast;
-using boost::format;
 using boost::assign::list_of;
-using std::string;
+using boost::format;
+using boost::lexical_cast;
 using std::cerr;
 using std::endl;
+using std::string;
 using std::vector;
 
 namespace po = boost::program_options;
@@ -119,7 +119,7 @@ bool Parameters::Load(int argc, char **argv) {
 
   if (argc == 1) {
     std::cerr << usage << std::endl;
-    return false;
+    throw std::invalid_argument("");
   }
 
   po::variables_map arg_map;
diff --git a/common/parameters.h b/common/parameters.h
index ac4f4b6..3484693 100644
--- a/common/parameters.h
+++ b/common/parameters.h
@@ -31,25 +31,29 @@
 #include "genotyping/short_repeat_genotyper.h"
 
 class Outputs {
-public:
+ public:
   Outputs(const std::string vcf_path, const std::string json_path,
           const std::string log_path);
   std::ostream &vcf() { return vcf_; }
   std::ostream &json() { return json_; }
   std::ostream &log() { return log_; }
 
-private:
+ private:
   std::ofstream vcf_;
   std::ofstream json_;
   std::ofstream log_;
 };
 
 class Parameters {
-public:
+ public:
   const double kSmallestPossibleDepth = 5.0;
   Parameters()
-      : region_extension_len_(1000), min_wp_(0.90), min_baseq_(20),
-        min_anchor_mapq_(60), skip_unaligned_(false), depth_(0.0),
+      : region_extension_len_(1000),
+        min_wp_(0.90),
+        min_baseq_(20),
+        min_anchor_mapq_(60),
+        skip_unaligned_(false),
+        depth_(0.0),
         sex_(Sex::kFemale) {}
   bool Load(int argc, char **argv);
   std::string bam_path() const { return bam_path_; }
@@ -73,7 +77,7 @@ class Parameters {
   bool depth_is_set() const { return depth_ >= kSmallestPossibleDepth; }
   Sex sex() const { return sex_; }
 
-private:
+ private:
   std::string bam_path_;
   std::string genome_path_;
   // Maximum distance from a region to search for relevant reads.
diff --git a/src/expansion_hunter.cc b/src/expansion_hunter.cc
index 3a528d2..eaa16dc 100644
--- a/src/expansion_hunter.cc
+++ b/src/expansion_hunter.cc
@@ -51,14 +51,14 @@
 #include "purity/purity.h"
 #include "rep_align/rep_align.h"
 
-using std::unordered_set;
-using std::map;
-using std::vector;
-using std::string;
+using std::array;
 using std::cerr;
 using std::endl;
+using std::map;
 using std::pair;
-using std::array;
+using std::string;
+using std::unordered_set;
+using std::vector;
 
 // Returns the length of the first read in a BAM file.
 size_t CalcReadLen(const string &bam_path) {
@@ -385,14 +385,12 @@ void EstimateRepeatSizes(const Parameters &parameters,
         haplotype_candidates.push_back(
             RepeatAllele(read_group.size, read_group.num_supporting_reads,
                          ReadType::kSpanning));
-
       } else if (read_group.read_type == ReadType::kInrepeat) {
         flanking_size_counts[num_units_in_read] +=
             read_group.num_supporting_reads;
         haplotype_candidates.push_back(
             RepeatAllele(num_units_in_read, read_group.num_supporting_reads,
                          ReadType::kInrepeat));
-
       } else if (read_group.read_type == ReadType::kFlanking) {
         haplotype_candidates.push_back(
             RepeatAllele(read_group.size, read_group.num_supporting_reads,
@@ -400,7 +398,6 @@ void EstimateRepeatSizes(const Parameters &parameters,
         for (const auto &align : read_group.rep_aligns) {
           flanking_size_counts[align.size] += 1;
         }
-
       } else {
         throw std::logic_error("Do not know how to deal with " +
                                kReadTypeToString.at(read_group.read_type) +
@@ -427,9 +424,10 @@ void EstimateRepeatSizes(const Parameters &parameters,
     cerr << "]" << endl;
 
     if (haplotype_candidates.empty()) {
-      cerr << TimeStamp()
-           << ",\t[Skipping this region because no informative reads were found]"
-           << endl;
+      cerr
+          << TimeStamp()
+          << ",\t[Skipping this region because no informative reads were found]"
+          << endl;
       continue;
     }
 
@@ -468,12 +466,13 @@ int main(int argc, char *argv[]) {
     cerr << kProgramVersion << endl;
 
     if (!parameters.Load(argc, argv)) {
-      return 1;
+      return 0;
     }
 
-    cerr << TimeStamp() << ",[Starting Logging for " << parameters.sample_name() << "]" << endl;
+    cerr << TimeStamp() << ",[Starting Logging for " << parameters.sample_name()
+         << "]" << endl;
 
-         Outputs outputs(parameters.vcf_path(), parameters.json_path(),
+    Outputs outputs(parameters.vcf_path(), parameters.json_path(),
                     parameters.log_path());
 
     map<string, RepeatSpec> repeat_specs;
@@ -498,7 +497,8 @@ int main(int argc, char *argv[]) {
       parameters.set_depth(depth);
     }
 
-    cerr << TimeStamp() << ",[Read length: " << parameters.read_len() << "]" << endl;
+    cerr << TimeStamp() << ",[Read length: " << parameters.read_len() << "]"
+         << endl;
     cerr << TimeStamp() << ",[Depth: " << parameters.depth() << "]" << endl;
 
     if (parameters.depth() < parameters.kSmallestPossibleDepth) {