From 320ae7ca70c270dd0a5002fdfc94307361c3956b Mon Sep 17 00:00:00 2001
From: yhoogstrate <y.hoogstrate@gmail.com>
Date: Tue, 3 Mar 2020 15:59:26 +0100
Subject: [PATCH] release notes v1.7.5

---
 CMakeLists.txt |  2 +-
 Changelog      | 10 ++++++++--
 src/main.cpp   | 17 ++++++++++++++++-
 3 files changed, 25 insertions(+), 4 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index ae7a45fc..e37568f0 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -8,7 +8,7 @@ project(fastafs)
 # Do this once in a while - find different bugs
 #set(CMAKE_CXX_COMPILER             "clang++")
 
-set(PROJECT_VERSION "1.7.4")
+set(PROJECT_VERSION "1.7.5")
 set(PACKAGE_URL "https://github.com/yhoogstrate/fastafs")
 set(PACKAGE_BUGREPORT "${PACKAGE_URL}/issues")
 
diff --git a/Changelog b/Changelog
index 36f8132e..6c5d1bef 100644
--- a/Changelog
+++ b/Changelog
@@ -1,9 +1,15 @@
-2020-20-27  Youri Hoogstrate
+2020-03-03  Youri Hoogstrate
+
+   * v1.7.5
+   * Added argument `check -5/--md5sum` to do file verification using md5sums as well
+   * Fixed error code returned after `fastafs check --help`
+
+2020-02-27  Youri Hoogstrate
 
    * v1.7.4
    * Added argument `cache --2bit` for statistical analysis
 
-2020-20-26  Youri Hoogstrate
+2020-02-26  Youri Hoogstrate
 
    * v1.7.3
    * Small decoy function added for basic snakemake compatiblity
diff --git a/src/main.cpp b/src/main.cpp
index 762967ca..8f2d92f4 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -61,6 +61,7 @@ void usage_check(void)
 {
     std::cout << "usage: " << PACKAGE << " check [<options>] <fastafs-id>\n\n";
     std::cout << "  -f, --file           Provide fastafs by file path, not from database (cache)" << std::endl;
+    std::cout << "  -5, --md5            Check file integrity using whole-file-CRC32 plus per-sequence MD5" << std::endl;
     std::cout << std::endl;
     std::cout << "  -h, --help           Display this help and exit";
     std::cout << std::endl;
@@ -272,12 +273,21 @@ int main(int argc, char *argv[])
             }
         } else if(strcmp(argv[1], "check") == 0) {
             if(argc > 2) {
+                if(strcmp(argv[2], "--help") == 0 or strcmp(argv[2], "-h") == 0) {
+                    usage_check();
+                    exit(0);
+                }
+                
                 bool from_file = false;
+                bool check_md5 = false;
 
                 for(int i = 2; i < argc - 1; i++) {
                     if(strcmp(argv[i], "-f") == 0 or strcmp(argv[i], "--file") == 0) {
                         from_file = true;
                     }
+                    else if (strcmp(argv[i], "-5") == 0 or strcmp(argv[i], "--md5") == 0) {
+                        check_md5 = true;
+                    }
                 }
 
                 std::string fname;
@@ -297,7 +307,12 @@ int main(int argc, char *argv[])
                 f.load(fname);
 
                 bool check1 = f.check_file_integrity(true);
-                bool check2 = f.check_sequence_integrity(true);
+                bool check2 = true;
+                
+                if(check_md5) {
+                    check2 = f.check_sequence_integrity(true);
+                }
+                
                 if(check1 and check2) {
                     return 0;
                 } else {