Modifications to compile #2
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This pull request includes the changes I made to successfully compile the repository using Intel's ifx compiler with MKL support.
Compilation
The default
Compile.shscript didn't work in my environment becauseiforcompiler is not availble, so I compiled the project using the following steps:Cloning
When cloning with
git clone --recurse-submodules https://github.com/AlphaGenes/AlphaPhase.gitthe three submodules,alphacmakefiles,alphaphase-doc, andalphahouse, are retrieved from BitBucket, which caused access issues on my end. I manually downloaded them from their respective GitHub repositories instead:Changes
Most changes were made to the linked repository and were necessary to address compilation errors or warnings. Below is a summary of the changes:
AlphaPhase/alphahouse/src/Utilities/LinkedListModule.f90Line 186: Removed pure statement (was causing compilation issues).
AlphaPhase/alphahouse/src/Utilities/HashModule.f90Line 222: Removed pure statement.
AlphaPhase/alphahouse/src/BioComputational/PedigreeModule.f90Line 1054: Added a new paragraph after &.
AlphaPhase/alphahouse/src/BioComputational/PedigreeModule.f90Line 1060: Added a new paragraph after &.
AlphaPhase/alphahouse/src/BioComputational/PedigreeModule.f90Line 1067: Added a new paragraph after &.
AlphaPhase/alphahouse/src/BioComputational/PedigreeModule.f90Line 1068: Added a new paragraph after &.
AlphaPhase/alphahouse/src/BioComputational/PedigreeModule.f90Line 1080: Added a new paragraph after &.
AlphaPhase/alphahouse/src/BioComputational/PedigreeModule.f90Line 1085: Added a new paragraph after &.
AlphaPhase/alphahouse/src/BioComputational/PedigreeModule.f90Line 1091: Added a new paragraph after &.
AlphaPhase/alphahouse/src/BioComputational/PedigreeModule.f90Line 1101: Added a new paragraph after &.
AlphaPhase/alphahouse/src/BioComputational/PedigreeModule.f90Line 1106: Added a new paragraph after &.
AlphaPhase/alphahouse/src/BioComputational/PedigreeModule.f90Line 1112: Added a new paragraph after &.
These changes were made to fix syntax/formatting errors with line continuation in Fortran.
AlphaPhase/alphahouse/src/Utilities/CompatibilityModule.f90Line 1213: Defined a temporary variable tmpBimInfo to temporarily store data returned from the createBimInfoFromGenotypes function.
AlphaPhase/alphahouse/src/Utilities/LineModule.f90Line 249: Removed pure statement.
AlphaPhase/alphahouse/src/Utilities/LineModule.f90Line 275: Removed pure statement.
AlphaPhase/src/MemberManagerModule.f90Line 136: Removed type-bound function call to getNAnisG() since it's not declared pure and thus not suitable in this context.
Output and Debugging Enhancement
17.
AlphaPhase/src/InputOutput.f90Lines 703-704: Modified to print all output results explicitly
New options and parameters
I could observed some new functions were explored (I'm not sure if they were completelly implemented) and the documentation has not yet been updated to reflect these recent changes in this software. In particular, new options such as printing results by cores instead of by genotype are currently not explained in the user guide or help documentation.
Feel free to invite me to collaborate (to the best of my knowledge) to continue contributing to the development and maintenance of these repositories and their respective documentation. I haven't wanted to make many changes in this pull request, as I know these are interconnected and highly developed packages, thus avoiding incompatibility issues, etc. I'd be happy to continue supporting you in any way necessary.