add VERBOSE

.github/workflows/mac.yml

@@ -2,7 +2,7 @@ name: MacOS
 
 on:
   push:
-    branches: [ main, dev ]
+    branches: [ main, doc ]
   pull_request:
     branches: [ main ]
 
@@ -23,8 +23,8 @@ jobs:
     - name: test
       run: |
         cd test
-        export LIBRARY_PATH="${LIBRARY_PATH}:$(brew --prefix)/lib"
-        export C_INCLUDE_PATH="${C_INCLUDE_PATH}:$(brew --prefix)/include"
-        export CPPFLAGS="-I"$(brew --prefix)/include
-        make
+        export LIBRARY_PATH=${LIBRARY_PATH}:$(brew --prefix)/lib
+        export C_INCLUDE_PATH=${C_INCLUDE_PATH}:$(brew --prefix)/include
+        export CPPFLAGS=-I"$(brew --prefix)/include"
+        make HTSINC=$(brew --prefix)/include HTSLIB=$(brew --prefix)/lib
         make test

Doxyfile

@@ -58,7 +58,7 @@ PROJECT_LOGO           =
 # entered, it will be relative to the location where doxygen was started. If
 # left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = /home/zilong/Projects/mysite/content/proj
+OUTPUT_DIRECTORY       = /home/zilong/Projects/mysite/public/proj
 
 # If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub-
 # directories (in 2 levels) under the output directory of each output format and

vcfpp.h

@@ -2,7 +2,7 @@
  * @file        https://github.com/Zilong-Li/vcfpp/vcfpp.h
  * @author      Zilong Li
  * @email       [email protected]
- * @version     v0.3.9
+ * @version     v0.4.0
  * @breif       a single C++ file for manipulating VCF
  * Copyright (C) 2022-2023.The use of this code is governed by the LICENSE file.
  ******************************************************************************/
@@ -497,7 +497,9 @@ class BcfRecord
         ret = bcf_get_genotypes(header->hdr, line.get(), &gts, &ndst);
         if(ret <= 0)
         {
+#    if defined(VERBOSE)
             std::cerr << "GT not present for current site. did you initilize the variant object?\n";
+#    endif
             return false;
         }
         // if nploidy is not set manually. find the max nploidy using the first variant (eg. 2) resize v as
@@ -568,7 +570,9 @@ class BcfRecord
         ret = bcf_get_genotypes(header->hdr, line.get(), &gts, &ndst);
         if(ret <= 0)
         {
+#    if defined(VERBOSE)
             std::cerr << "GT not present for current site. did you initilize the variant object?\n";
+#    endif
             return false;
         }
         v.resize(ret);
@@ -767,8 +771,10 @@ class BcfRecord
         }
         else
         {
+#    if defined(VERBOSE)
             std::cerr << "there are multiple values for " + tag
                              + " in INFO for current site. please use vector instead\n";
+#    endif
             return false;
         }
     }
@@ -825,7 +831,9 @@ class BcfRecord
         }
         if(ret < 0)
         {
+#    if defined(VERBOSE)
             std::cerr << "couldn't set " + tag + " for this variant.\nplease add the tag in headerfirst.\n";
+#    endif
             return false;
         }
         return true;
@@ -861,7 +869,9 @@ class BcfRecord
 
         if(ret < 0)
         {
+#    if defined(VERBOSE)
             std::cerr << "couldn't set " + tag + " for this variant.\nplease add the tag in headerfirst.\n";
+#    endif
             return false;
         }
         return true;
@@ -927,7 +937,9 @@ class BcfRecord
         if(bcf_update_genotypes(header->hdr, line.get(), gt, v.size()) < 0)
         {
             free(gt);
+#    if defined(VERBOSE)
             std::cerr << "couldn't set genotypes correctly.\n";
+#    endif
             return false;
         }
         free(gt);
@@ -994,7 +1006,9 @@ class BcfRecord
 
         if(ret < 0)
         {
+#    if defined(VERBOSE)
             std::cerr << "couldn't set format " + tag + " corectly.\n";
+#    endif
             return false;
         }
         return true;
@@ -1026,7 +1040,9 @@ class BcfRecord
         }
         if(ret < 0)
         {
+#    if defined(VERBOSE)
             std::cerr << "couldn't set format " + tag + " corectly.\n";
+#    endif
             return false;
         }
         return true;