[Genabel-commits] r2015 - in pkg/ProbABEL: doc src

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2015-09-21 14:33:14 +0200 (Mon, 21 Sep 2015)
New Revision: 2015

Added:
   pkg/ProbABEL/doc/extract-snp.1
Modified:
   pkg/ProbABEL/doc/Makefile.am
   pkg/ProbABEL/src/extract-snp.cpp
Log:
ProbABEL: Added manual page for extract-snp tool.
Also fixed minor typo in the help text of extract-snp.


Modified: pkg/ProbABEL/doc/Makefile.am
===================================================================
--- pkg/ProbABEL/doc/Makefile.am	2015-08-20 07:11:59 UTC (rev 2014)
+++ pkg/ProbABEL/doc/Makefile.am	2015-09-21 12:33:14 UTC (rev 2015)
@@ -16,6 +16,9 @@
 if BUILD_pacoxph
 man_MANS += pacoxph.1
 endif
+if BUILD_extractsnp
+man_MANS += extract-snp.1
+endif
 
 EXTRA_DIST = $(man_MANS)
 

Added: pkg/ProbABEL/doc/extract-snp.1
===================================================================
--- pkg/ProbABEL/doc/extract-snp.1	                        (rev 0)
+++ pkg/ProbABEL/doc/extract-snp.1	2015-09-21 12:33:14 UTC (rev 2015)
@@ -0,0 +1,54 @@
+.TH extract-snp 1 "21 September 2015" "ProbABEL 0.4.5"
+.SH NAME
+extract-snp \- tool to extract dosage values for a given SNP for all or some individuals.
+.SH SYNOPSIS
+.B extract-snp
+.B "-f\ \fIFILE\fR"
+.B "-s\ \fISNPNAME\fR"
+.RI "[" "OPTIONS" "]"
+.SH DESCRIPTION
+.B extract-snp
+extracts the dosage for a SNP for one or more individuals from a file in filevector
+format (.fvi/.fvd).
+.PP
+.SH OPTIONS
+.SS Required command line options
+.TP
+.BI "-f, \-\^\-file" " FILE"
+Name of the filevector file from which to extract the dosages. This
+can be either the file with the .fvi or the .fvd extension.
+.TP
+.BI "-s, \-\^\-snp" " snpname"
+Name of the SNP or variant for which to extract the dosages
+.RE
+.SS Other, non-mandatory options
+.TP
+.BI "-i, \-\^\-id" " individualID"
+Extract the dosage for only one individual (with ID
+\fIindividualID\fR) for the SNP listed with the \-\-snp option.
+.RE
+.TP
+.BI "-h, \-\^\-help"
+Print usage information to the screen and exit.
+.RE
+.TP
+.BI "-d, \-\^\-debug"
+Turn on debug mode. This will print a lot of extra output to the
+screen, for example it lists the names of all individuals and SNPs
+found in the file.
+.RE
+.SH EXAMPLES
+This extracts the dosages for all individuals:
+.nf
+.RS
+extract-snp \-f ../checks/inputfiles/mmscore_gen.dose.fvi \-s  rs70099 > dosage.txt
+.RE
+.fi
+.SH "SEE ALSO"
+palinear(1), palogist(1), pacoxph(1), probabel(1), and the R package DatABEL.
+.SH BUGS
+The bugtracker is located at
+.br
+https://r-forge.r-project.org/tracker/?group_id=505
+.SH AUTHORS
+Lennart C. Karssen

Modified: pkg/ProbABEL/src/extract-snp.cpp
===================================================================
--- pkg/ProbABEL/src/extract-snp.cpp	2015-08-20 07:11:59 UTC (rev 2014)
+++ pkg/ProbABEL/src/extract-snp.cpp	2015-09-21 12:33:14 UTC (rev 2015)
@@ -40,7 +40,7 @@
 {
     cout << program_name
          << " extracts the dosage for a SNP for one or more individuals from a"
-         << "file in filevector format (.fvi/.fvd)." << endl;
+         << " file in filevector format (.fvi/.fvd)." << endl;
     cout << endl;
     cout << "Usage: " << program_name << " --file <fv file> --snp <snpname>"
          << endl;
@@ -121,6 +121,7 @@
 
     if (debug)
     {
+        // Print all individual names
         for (unsigned long int col = 0; col < fv.getNumObservations(); col++)
         {
             cout << fv.readObservationName(col).name << " ";