clean import

zqfang · Aug 14, 2024 · 562be52 · 562be52
1 parent b80056c
commit 562be52
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Showing 10 changed files with 30 additions and 57 deletions.
diff --git a/haplomap/include/constants.h b/haplomap/include/constants.h
@@ -2,8 +2,8 @@
 // Created by Zhuoqing Fang on 8/13/24.
 //
 // #pragma once
-#ifndef CONFIG_H
-#define CONFIG_H
+#ifndef CONSTANTS_H
+#define CONSTANTS_H
 
 #include <string>
 #include <unordered_map>

diff --git a/haplomap/include/eigen.h b/haplomap/include/eigen.h
@@ -2,8 +2,8 @@
 // Created by Zhuoqing Fang on 7/8/20.
 //
 
-#ifndef HBCGM_EIGEN_H
-#define HBCGM_EIGEN_H
+#ifndef EIGEN_H
+#define EIGEN_H
 #include <vector>
 #include <string>
 #include "dynum.h"
@@ -38,4 +38,4 @@ struct EigenMat
     gsl_matrix* pca(unsigned int L);
 };
 
-#endif //HBCGM_EIGEN_H
+#endif // EIGEN_H
diff --git a/haplomap/include/haplolib.h b/haplomap/include/haplolib.h
@@ -1,5 +1,6 @@
 // -*-c++-*-
-
+#ifndef HAPLOLIB_H
+#define HAPLOLIB_H
 // Various useful functions from nhaploblocks
 //#pragma once
 #include <fstream>
@@ -185,3 +186,4 @@ extern Dynum<std::string> chromosomes;
 // vector of all good SNPs in order of chromosome, position.
 extern std::vector<SNPInfo *> snpVec;
 
+#endif
diff --git a/haplomap/include/haplomap.h b/haplomap/include/haplomap.h
@@ -2,8 +2,8 @@
 // Created by Zhuoqing Fang on 7/11/20.
 //
 #pragma once
-#ifndef HBCGM_HAPLOMAP_H
-#define HBCGM_HAPLOMAP_H
+#ifndef HAPLOMAP_H
+#define HAPLOMAP_H
 
 #include <getopt.h>
 #include <cstring>
@@ -23,4 +23,4 @@ int main_ghmap(int argc, char **argv);
 /// genetic relation matrix, see pca.cpp
 int main_eigen(int argc, char **argv);
 
-#endif //HBCGM_HAPLOMAP_H
+#endif // HAPLOMAP_H
diff --git a/haplomap/include/linalg.h b/haplomap/include/linalg.h
@@ -2,8 +2,8 @@
 // Created by Zhuoqing Fang on 7/8/20.
 //
 
-#ifndef HBCGM_LINALG_H
-#define HBCGM_LINALG_H
+#ifndef LINALG_H
+#define LINALG_H
 #include <vector>
 #include <assert.h>
 
@@ -66,4 +66,4 @@ std::vector<size_t> argsort(_RAIter first, _RAIter last, _Compare comp) {
 
 
 
-#endif //HBCGM_LINALG_H
+#endif // LINALG_H
diff --git a/haplomap/include/stats.h b/haplomap/include/stats.h
@@ -2,8 +2,8 @@
 // Created by Zhuoqing Fang on 7/6/20.
 //
 
-#ifndef HBCGM_STATS_H
-#define HBCGM_STATS_H
+#ifndef STATS_H
+#define STATS_H
 
 #include <iostream>
 #include <vector>
@@ -185,4 +185,4 @@ std::vector<bool> bh_fdr(std::vector<_NumericType>& pval, std::vector<_NumericTy
  */
 void bh_fdr(std::vector<BlockSummary *> & pval, float alpha=0.05, bool flag = 1);
 
-#endif //HBCGM_STATS_H
+#endif //STATS_H
diff --git a/haplomap/include/vcf.h b/haplomap/include/vcf.h
@@ -1,6 +1,8 @@
 //
 // Created by Zhuoqing Fang on 2/22/21.
 //
+#ifndef VCF_H
+#define VCF_H
 
 #include <memory>
 #include <iostream>
@@ -111,4 +113,6 @@ class VCF
     // read input file
     std::istream* input;
     VCFOptions* opts;
-};
+};
+
+#endif
diff --git a/haplomap/include/vep.h b/haplomap/include/vep.h
@@ -7,6 +7,8 @@
 // A deletion is indicated by the exact nucleotide coordinates. For example, a three base pair deletion of nucleotides 12600, 12601, and 12602 of the reverse strand will have start and end coordinates of :
 //    12600     12602 
 // see here: https://useast.ensembl.org/info/genome/variation/prediction/classification.html#classes
+#ifndef VEP_H
+#define VEP_H
 
 #include <memory>
 #include <iostream>
@@ -105,4 +107,6 @@ class VarirantEeffectPredictor
     void writeVEPImpact(char* outFileName);
     void writeVEPCsq(char* outFileName);
     bool getline(std::string &);
-};
+};
+
+#endif
diff --git a/haplomap/src/ghmap.cpp b/haplomap/src/ghmap.cpp
@@ -15,45 +15,8 @@ std::vector<BlockSummary *> blocks;                       // global vector of al
 std::vector<std::string> geneExprHeader;
 int traceFStat = false;
 
-// std::unordered_map<std::string, int> PRIOR = {{"HIGH", 2}, {"MODERATE", 1}, {"LOW", 0}, {"MODIFIER", -1}};
-// std::unordered_map<std::string, int> CSQs = {
-//     {"transcript_ablation", 2},
-//     {"splice_acceptor_variant", 2},
-//     {"splice_donor_variant", 2},
-//     {"stop_gained", 2},
-//     {"frameshift_variant", 2},
-//     {"stop_lost", 2},
-//     {"start_lost", 2},
-//     {"transcript_amplification", 2},
-//     {"inframe_insertion", 1},
-//     {"inframe_deletion", 1},
-//     {"missense_variant", 1},
-//     {"protein_altering_variant", 1},
-//     {"splice_region_variant", 0},
-//     {"incomplete_terminal_codon_variant", 0},
-//     {"start_retained_variant", 0},
-//     {"stop_retained_variant", 0},
-//     {"synonymous_variant", 0},
-//     {"coding_sequence_variant", -1},
-//     {"mature_miRNA_variant", -1},
-//     {"5_prime_UTR_variant", -1},
-//     {"3_prime_UTR_variant", -1},
-//     {"non_coding_transcript_exon_variant", -1},
-//     {"intron_variant", -1},
-//     {"NMD_transcript_variant", -1},
-//     {"non_coding_transcript_variant", -1},
-//     {"upstream_gene_variant", -1},
-//     {"downstream_gene_variant", -1},
-//     {"TFBS_ablation", -1},
-//     {"TFBS_amplification", -1},
-//     {"TF_binding_site_variant", -1},
-//     {"regulatory_region_ablation", -1},
-//     {"regulatory_region_amplification", -1},
-//     {"feature_elongation", -1},
-//     {"regulatory_region_variant", -1},
-//     {"feature_truncation", -1},
-//     {"intergenic_variant", -1},
-// };
+// std::unordered_map<std::string, int> PRIOR // from constants.h;
+// std::unordered_map<std::string, int> CSQs // from constants.h
 
 // constructor
 BlockSummary::BlockSummary(const char *chrnm, int num, int start, int size,

diff --git a/haplomap/src/vep.cpp b/haplomap/src/vep.cpp
@@ -320,7 +320,7 @@ void VarirantEeffectPredictor::readVEP(char *inVEPName, char *delemiter, char* v
 }
 std::string VarirantEeffectPredictor::codonChange(VEPSummary * pRecord)
 {   // aggregate all condon changes groupby (location, transcript)
-    std::string _expr = "";
+    std::string _expr;
     for (int j = 0; j < pRecord->codons.size(); j++)
     {
         std::string codon = pRecord->codons.eltOf(j);