[Genabel-commits] r860 - in pkg/ProbABEL: . src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Mar 26 21:27:49 CEST 2012
Author: lckarssen
Date: 2012-03-26 21:27:49 +0200 (Mon, 26 Mar 2012)
New Revision: 860
Modified:
pkg/ProbABEL/configure.ac
pkg/ProbABEL/src/main.cpp
Log:
ProbABEL:
- Set version to 1.99 (to indicate 0.2.0 beta, but this makes upgrading of Debian/Ubuntu packages easier). (configure.ac)
- Fixed a few spelling errors and clarified code layout (src/main.cpp)
Modified: pkg/ProbABEL/configure.ac
===================================================================
--- pkg/ProbABEL/configure.ac 2012-03-26 18:46:02 UTC (rev 859)
+++ pkg/ProbABEL/configure.ac 2012-03-26 19:27:49 UTC (rev 860)
@@ -2,8 +2,8 @@
# Process this file with autoconf to produce a configure script.
AC_PREREQ([2.67])
-AC_INIT(ProbABEL, 0.2.0-beta, genabel-devel at r-forge.wu-wien.ac.at)
-AM_INIT_AUTOMAKE(ProbABEL, 0.2.0-beta)
+AC_INIT(ProbABEL, 0.1.99, genabel-devel at r-forge.wu-wien.ac.at)
+AM_INIT_AUTOMAKE(ProbABEL, 0.1.99)
AC_CONFIG_SRCDIR([src/data.h])
AC_CONFIG_HEADERS([src/config.h])
Modified: pkg/ProbABEL/src/main.cpp
===================================================================
--- pkg/ProbABEL/src/main.cpp 2012-03-26 18:46:02 UTC (rev 859)
+++ pkg/ProbABEL/src/main.cpp 2012-03-26 19:27:49 UTC (rev 860)
@@ -196,7 +196,7 @@
}
if (score) {
- cout << "option --score supressed from v 0.1-6\n";
+ cout << "option --score suppressed from v 0.1-6\n";
exit(1);
}
@@ -311,14 +311,22 @@
*/
#if COXPH
- if(inverse_filename != NULL) {std::cerr<<"ERROR: mmscore is forbidden for cox regression\n";exit(1);}
- if (robust) {std::cerr<<"ERROR: robust standard errors not implemented for Cox regression (drop us e-mail if you really need that)\n";exit(1);}
+ if(inverse_filename != NULL)
+ {
+ std::cerr<<"ERROR: mmscore is forbidden for cox regression\n";
+ exit(1);
+ }
+ if (robust)
+ {
+ std::cerr<<"ERROR: robust standard errors not implemented for Cox regression\n";
+ exit(1);
+ }
#endif
if(inverse_filename != NULL)
{
- std::cout<<"you are runing mmscore...\n";
+ std::cout<<"you are running mmscore...\n";
}
std::cout << "Reading data ...";
@@ -438,11 +446,30 @@
- if (!outfile[0]->is_open()) {std::cerr << "Can not open file for writing: " << outfilename_str+"_2df.out.txt" << "\n"; exit(1);}
- if (!outfile[1]->is_open()) {std::cerr << "Can not open file for writing: " << outfilename_str+"_add.out.txt" << "\n"; exit(1);}
- if (!outfile[2]->is_open()) {std::cerr << "Can not open file for writing: " << outfilename_str+"_domin.out.txt" << "\n"; exit(1);}
- if (!outfile[3]->is_open()) {std::cerr << "Can not open file for writing: " << outfilename_str+"_recess.out.txt" << "\n"; exit(1);}
- if (!outfile[4]->is_open()) {std::cerr << "Can not open file for writing: " << outfilename_str+"_over_domin.out.txt" << "\n"; exit(1);}
+ if (!outfile[0]->is_open())
+ {
+ std::cerr << "Cannot open file for writing: " << outfilename_str+"_2df.out.txt" << "\n";
+ exit(1);
+ }
+ if (!outfile[1]->is_open())
+ {
+ std::cerr << "Cannot open file for writing: " << outfilename_str+"_add.out.txt" << "\n";
+ exit(1);}
+ if (!outfile[2]->is_open())
+ {
+ std::cerr << "Cannot open file for writing: " << outfilename_str+"_domin.out.txt" << "\n";
+ exit(1);
+ }
+ if (!outfile[3]->is_open())
+ {
+ std::cerr << "Cannot open file for writing: " << outfilename_str+"_recess.out.txt" << "\n";
+ exit(1);
+ }
+ if (!outfile[4]->is_open())
+ {
+ std::cerr << "Cannot open file for writing: " << outfilename_str+"_over_domin.out.txt" << "\n";
+ exit(1);
+ }
//_____________________
@@ -450,8 +477,9 @@
//_____________________
for(int i=0 ; i<outfile.size() ; i++)
{
- (*outfile[i]) << "name" << sep << "A1" << sep << "A2" << sep << "Freq1" << sep << "MAF" << sep << "Quality" << sep << "Rsq"
- << sep << "n" << sep << "Mean_predictor_allele";
+ (*outfile[i]) << "name" << sep << "A1" << sep << "A2" << sep << "Freq1" << sep << "MAF"
+ << sep << "Quality" << sep << "Rsq" << sep << "n" << sep
+ << "Mean_predictor_allele";
if (chrom != "-1") (*outfile[i]) << sep << "chrom";
if (mapfilename != NULL) (*outfile[i]) << sep << "position";
}
@@ -461,9 +489,12 @@
{
for (int file=0; file<outfile.size() ; file++)
for (int i =0; i<phd.n_model_terms-1;i++)
- *outfile[file] << sep << "beta_" << phd.model_terms[i] << sep << "sebeta_" << phd.model_terms[i];
+ *outfile[file] << sep << "beta_" << phd.model_terms[i] << sep
+ << "sebeta_" << phd.model_terms[i];
}
- *outfile[0] << sep << "beta_SNP_A1A2" << sep << "beta_SNP_A1A1" << sep << "sebeta_SNP_A1A2" << sep << "sebeta_SNP_A1A1";
+ *outfile[0] << sep << "beta_SNP_A1A2" << sep << "beta_SNP_A1A1" << sep
+ << "sebeta_SNP_A1A2" << sep << "sebeta_SNP_A1A1";
+
*outfile[1] << sep << "beta_SNP_addA1" << sep << "sebeta_SNP_addA1";
*outfile[2] << sep << "beta_SNP_domA1" << sep << "sebeta_SNP_domA1";
*outfile[3] << sep << "beta_SNP_recA1" << sep << "sebeta_SNP_recA1";
@@ -472,19 +503,28 @@
if(interaction != 0)
{
//Han Chen
- *outfile[0] << sep << "beta_SNP_A1A2_" << phd.model_terms[interaction_cox] << sep << "sebeta_SNP_A1A2_" << phd.model_terms[interaction_cox]
- << sep << "beta_SNP_A1A1_" << phd.model_terms[interaction_cox] << sep << "sebeta_SNP_A1A1_" << phd.model_terms[interaction_cox];
+ *outfile[0] << sep << "beta_SNP_A1A2_" << phd.model_terms[interaction_cox] << sep
+ << "sebeta_SNP_A1A2_" << phd.model_terms[interaction_cox]
+ << sep << "beta_SNP_A1A1_" << phd.model_terms[interaction_cox] << sep
+ << "sebeta_SNP_A1A1_" << phd.model_terms[interaction_cox];
#if !COXPH
- if(inverse_filename == NULL && !allcov) *outfile[0] << sep << "cov_SNP_A1A2_int_SNP_" << phd.model_terms[interaction_cox]
- << sep << "cov_SNP_A1A1_int_SNP_" << phd.model_terms[interaction_cox];
+ if(inverse_filename == NULL && !allcov)
+ {
+ *outfile[0] << sep << "cov_SNP_A1A2_int_SNP_" << phd.model_terms[interaction_cox]
+ << sep << "cov_SNP_A1A1_int_SNP_" << phd.model_terms[interaction_cox];
+ }
#endif
//Oct 26, 2009
for (int file=1; file<outfile.size() ; file++)
{
- *outfile[file] << sep << "beta_SNP_" << phd.model_terms[interaction_cox] << sep << "sebeta_SNP_" << phd.model_terms[interaction_cox];
+ *outfile[file] << sep << "beta_SNP_" << phd.model_terms[interaction_cox] << sep
+ << "sebeta_SNP_" << phd.model_terms[interaction_cox];
//Han Chen
#if !COXPH
- if(inverse_filename == NULL && !allcov) *outfile[file] << sep << "cov_SNP_int_SNP_" << phd.model_terms[interaction_cox];
+ if(inverse_filename == NULL && !allcov)
+ {
+ *outfile[file] << sep << "cov_SNP_int_SNP_" << phd.model_terms[interaction_cox];
+ }
#endif
//Oct 26, 2009
}
@@ -520,8 +560,8 @@
//Header
//_____________________
- *outfile[0] << "name" << sep << "A1" << sep << "A2" << sep << "Freq1" << sep << "MAF" << sep << "Quality" << sep << "Rsq"
- << sep << "n" << sep << "Mean_predictor_allele";
+ *outfile[0] << "name" << sep << "A1" << sep << "A2" << sep << "Freq1" << sep << "MAF" << sep
+ << "Quality" << sep << "Rsq" << sep << "n" << sep << "Mean_predictor_allele";
if (chrom != "-1") *outfile[0] << sep << "chrom";
if (mapfilename != NULL) *outfile[0] << sep << "position";
//_____________________
@@ -530,21 +570,30 @@
if(allcov) //All covariates in output
{
for (int i =0; i<phd.n_model_terms-1;i++)
- *outfile[0] << sep << "beta_" << phd.model_terms[i] << sep << "sebeta_" << phd.model_terms[i];
-
+ {
+ *outfile[0] << sep << "beta_" << phd.model_terms[i] << sep << "sebeta_"
+ << phd.model_terms[i];
+ }
*outfile[0] << sep << "beta_SNP_add" << sep << "sebeta_SNP_add";
}
else //Only beta, sebeta for additive model go to output file
{
*outfile[0] << sep << "beta_SNP_add" << sep << "sebeta_SNP_add";
}
- if(interaction != 0) *outfile[0] << sep << "beta_SNP_" << phd.model_terms[interaction_cox] << sep << "sebeta_SNP_" << phd.model_terms[interaction_cox];
+ if(interaction != 0)
+ {
+ *outfile[0] << sep << "beta_SNP_" << phd.model_terms[interaction_cox] << sep
+ << "sebeta_SNP_" << phd.model_terms[interaction_cox];
+ }
if(inverse_filename == NULL)
//Han Chen
{
#if !COXPH
- if(interaction != 0 && !allcov) *outfile[0] << sep << "cov_SNP_int_SNP_" << phd.model_terms[interaction_cox];
+ if(interaction != 0 && !allcov)
+ {
+ *outfile[0] << sep << "cov_SNP_int_SNP_" << phd.model_terms[interaction_cox];
+ }
#endif
*outfile[0] << sep << "loglik"; //"chi2_SNP";
}
@@ -580,11 +629,30 @@
- if (!outfile[0]->is_open()) {std::cerr << "Can not open file for writing: " << outfilename_str+"_2df.out.txt" << "\n"; exit(1);}
- if (!outfile[1]->is_open()) {std::cerr << "Can not open file for writing: " << outfilename_str+"_add.out.txt" << "\n"; exit(1);}
- if (!outfile[2]->is_open()) {std::cerr << "Can not open file for writing: " << outfilename_str+"_domin.out.txt" << "\n"; exit(1);}
- if (!outfile[3]->is_open()) {std::cerr << "Can not open file for writing: " << outfilename_str+"_recess.out.txt" << "\n"; exit(1);}
- if (!outfile[4]->is_open()) {std::cerr << "Can not open file for writing: " << outfilename_str+"_over_domin.out.txt" << "\n"; exit(1);}
+ if (!outfile[0]->is_open()) {
+ std::cerr << "Cannot open file for writing: " << outfilename_str+"_2df.out.txt" << "\n";
+ exit(1);
+ }
+ if (!outfile[1]->is_open())
+ {
+ std::cerr << "Cannot open file for writing: " << outfilename_str+"_add.out.txt" << "\n";
+ exit(1);
+ }
+ if (!outfile[2]->is_open())
+ {
+ std::cerr << "Cannot open file for writing: " << outfilename_str+"_domin.out.txt" << "\n";
+ exit(1);
+ }
+ if (!outfile[3]->is_open())
+ {
+ std::cerr << "Cannot open file for writing: " << outfilename_str+"_recess.out.txt" << "\n";
+ exit(1);
+ }
+ if (!outfile[4]->is_open())
+ {
+ std::cerr << "Cannot open file for writing: " << outfilename_str+"_over_domin.out.txt" << "\n";
+ exit(1);
+ }
}
else
{
@@ -867,7 +935,8 @@
{
//Write mlinfo to output:
*outfile[0] << mli.name[csnp] << sep << mli.A1[csnp] << sep << mli.A2[csnp] << sep;
- *outfile[0] << mli.Freq1[csnp] << sep << mli.MAF[csnp] << sep << mli.Quality[csnp] << sep << mli.Rsq[csnp] << sep;
+ *outfile[0] << mli.Freq1[csnp] << sep << mli.MAF[csnp] << sep << mli.Quality[csnp] << sep
+ << mli.Rsq[csnp] << sep;
*outfile[0] << gcount << sep << freq;
if (chrom != "-1") *outfile[0] << sep << chrom;
if (mapfilename != NULL) *outfile[0] << sep << mli.map[csnp];
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