Added .gitignore file back

[rsem.git] / WriteResults.h

diff --git a/WriteResults.h b/WriteResults.h
index 95aa7b0b12251b1527c859d132970a26e3fdd5dd..79ba5b2d0449cadfc57c771c8104d7896906074e 100644 (file)
--- a/WriteResults.h
+++ b/WriteResults.h
@@ -1,6 +1,7 @@
 #ifndef WRITERESULTS_H_
 #define WRITERESULTS_H_
 
+#include<cmath>
 #include<cstdio>
 #include<vector>
 #include<string>
@@ -336,28 +337,16 @@ void writeResultsEM(int M, const char* refName, const char* imdName, Transcripts
        if (verbose) { printf("Expression Results are written!\n"); }
 }
 
-void writeResultsGibbs(int M, char* refName, char* imdName, std::vector<double>& pme_c, std::vector<double>& pme_fpkm, std::vector<double>& pme_tpm) {
+void writeResultsGibbs(int M, int m, int m_trans, GroupInfo& gi, GroupInfo &gt, GroupInfo &ta, bool alleleS, char* imdName, std::vector<double>& pme_c, std::vector<double>& pme_fpkm, std::vector<double>& pme_tpm, std::vector<double>& pve_c, std::vector<double>& pve_c_genes, std::vector<double>& pve_c_trans) {
        char outF[STRLEN];
        FILE *fo;
 
-       int m;
-       GroupInfo gi;
-       char groupF[STRLEN];
        std::vector<double> isopct;
        std::vector<double> gene_counts, gene_tpm, gene_fpkm;
 
-       // Load group info
-       sprintf(groupF, "%s.grp", refName);
-       gi.load(groupF);
-       m = gi.getm();
-
        // For allele-specific expression
-       int m_trans = 0;
-       GroupInfo gt, ta;
        std::vector<double> trans_counts, trans_tpm, trans_fpkm, ta_pct, gt_pct;
 
-       bool alleleS = isAlleleSpecific(refName, &gt, &ta); // if allele-specific
-
        //calculate IsoPct, etc.
        isopct.assign(M + 1, 0.0);
        gene_counts.assign(m, 0.0); gene_tpm.assign(m, 0.0); gene_fpkm.assign(m, 0.0);
@@ -375,7 +364,6 @@ void writeResultsGibbs(int M, char* refName, char* imdName, std::vector<double>&
        }
 
        if (alleleS) {
-         m_trans = ta.getm();
          ta_pct.assign(M + 1, 0.0);
          trans_counts.assign(m_trans, 0.0); trans_tpm.assign(m_trans, 0.0); trans_fpkm.assign(m_trans, 0.0);
          
@@ -407,6 +395,8 @@ void writeResultsGibbs(int M, char* refName, char* imdName, std::vector<double>&
          
          for (int i = 1; i <= M; i++)
            fprintf(fo, "%.2f%c", pme_c[i], (i < M ? '\t' : '\n'));
+         for (int i = 1; i <= M; i++) 
+           fprintf(fo, "%.2f%c", sqrt(pve_c[i]), (i < M ? '\t' : '\n'));
          for (int i = 1; i <= M; i++)
            fprintf(fo, "%.2f%c", pme_tpm[i], (i < M ? '\t' : '\n'));
          for (int i = 1; i <= M; i++)
@@ -423,6 +413,8 @@ void writeResultsGibbs(int M, char* refName, char* imdName, std::vector<double>&
          
          for (int i = 1; i <= M; i++)
            fprintf(fo, "%.2f%c", pme_c[i], (i < M ? '\t' : '\n'));
+         for (int i = 1; i <= M; i++) 
+           fprintf(fo, "%.2f%c", sqrt(pve_c[i]), (i < M ? '\t' : '\n'));
          for (int i = 1; i <= M; i++)
            fprintf(fo, "%.2f%c", pme_tpm[i], (i < M ? '\t' : '\n'));
          for (int i = 1; i <= M; i++)
@@ -440,6 +432,8 @@ void writeResultsGibbs(int M, char* refName, char* imdName, std::vector<double>&
          
          for (int i = 0; i < m_trans; i++)
            fprintf(fo, "%.2f%c", trans_counts[i], (i < m_trans - 1 ? '\t' : '\n'));
+         for (int i = 0; i < m_trans; i++) 
+           fprintf(fo, "%.2f%c", sqrt(pve_c_trans[i]), (i < m_trans - 1 ? '\t' : '\n'));
          for (int i = 0; i < m_trans; i++)
            fprintf(fo, "%.2f%c", trans_tpm[i], (i < m_trans - 1 ? '\t' : '\n'));
          for (int i = 0; i < m_trans; i++)
@@ -455,11 +449,13 @@ void writeResultsGibbs(int M, char* refName, char* imdName, std::vector<double>&
        general_assert(fo != NULL, "Cannot open " + cstrtos(outF) + "!");
 
        for (int i = 0; i < m; i++)
-               fprintf(fo, "%.2f%c", gene_counts[i], (i < m - 1 ? '\t' : '\n'));
+         fprintf(fo, "%.2f%c", gene_counts[i], (i < m - 1 ? '\t' : '\n'));
+       for (int i = 0; i < m; i++) 
+         fprintf(fo, "%.2f%c", sqrt(pve_c_genes[i]), (i < m - 1 ? '\t' : '\n'));
        for (int i = 0; i < m; i++)
-               fprintf(fo, "%.2f%c", gene_tpm[i], (i < m - 1 ? '\t' : '\n'));
+         fprintf(fo, "%.2f%c", gene_tpm[i], (i < m - 1 ? '\t' : '\n'));
        for (int i = 0; i < m; i++)
-               fprintf(fo, "%.2f%c", gene_fpkm[i], (i < m - 1 ? '\t' : '\n'));
+         fprintf(fo, "%.2f%c", gene_fpkm[i], (i < m - 1 ? '\t' : '\n'));
        fclose(fo);
 
        if (verbose) { printf("Gibbs based expression values are written!\n"); }