[med-svn] [Git][med-team/marginphase][master] Fix marginPhase.1 and write new vcfCompare.1

[Shayan Doust]

Shayan Doust pushed to branch master at Debian Med / marginphase


Commits:
49e3cff9 by Shayan Doust at 2020-07-01T18:19:52+01:00
Fix marginPhase.1 and write new vcfCompare.1

- - - - -


2 changed files:

- debian/mans/marginPhase.1
- + debian/mans/vcfCompare.1


Changes:

=====================================
debian/mans/marginPhase.1
=====================================
@@ -1,7 +1,7 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
-.TH USAGE: "1" "June 2020" "usage: marginPhase <BAM> <REFERENCE_FASTA> <PARAMS> [options]" "User Commands"
+.TH MARGINPHASE "1" "June 2020" "marginPhase" "User Commands"
 .SH NAME
-usage: \- Simultaneous haplotyping and genotyping
+marginPhase \- Simultaneous haplotyping and genotyping
 .SH DESCRIPTION
 usage: marginPhase <BAM> <REFERENCE_FASTA> <PARAMS> [options]
 Version: 1.0.0
@@ -103,13 +103,13 @@ so reads that aren't in SNP dir are discarded
 example: 0 \-> N/A; 2 \-> LFP; 7 \-> LTP,LFP,LFN)
 .SH "SEE ALSO"
 The full documentation for
-.B usage:
+.B marginPhase
 is maintained as a Texinfo manual.  If the
 .B info
 and
-.B usage:
+.B marginPhase
 programs are properly installed at your site, the command
 .IP
-.B info usage:
+.B info marginPhase
 .PP
 should give you access to the complete manual.


=====================================
debian/mans/vcfCompare.1
=====================================
@@ -0,0 +1,23 @@
+.\" Text automatically generated by txt2man and modified by hand
+.TH VCFCOMPARE  "01 July 2020" "vcfCompare" "User Commands"
+.SH NAME
+vcfCompare \- Compares VCF_EVALUATED to VCF_REFERENCE
+.SH SYNOPSIS
+.B vcfCompare
+[options] \fB-r\fP \fI\,VCF_REFERENCE\/\fR \fB-e\fP \fI\,VCF_EVALUATED\/\fR 
+
+\fB-h\fP \fB--help\fP : Print this help screen
+
+\fB-a\fP \fB--logLevel\fP : Set the log level
+
+\fB-r\fP \fB--vcfReference\fP : Specify reference VCF
+
+\fB-e\fP \fB--vcfEvaluated\fP : Specify evaluated VCF
+.SH DESCRIPTION
+Compares VCF_REFERENCE to VCF_REFERENCE using the following metrics:
+.IP 1. 4
+The concordance of all calls in VCF_REFERENCE compared to VCF_EVALUATED
+.IP 2. 4
+The concordance of all reference positions in VCF_REFERENCE compared to VCF_EVALUATED
+.IP 3. 4
+The phasing in VCF_REFERENCE compared to VCF_EVALUATED



View it on GitLab: https://salsa.debian.org/med-team/marginphase/-/commit/49e3cff9a7fd895c1d5274527d2d4316396ee2b9

-- 
View it on GitLab: https://salsa.debian.org/med-team/marginphase/-/commit/49e3cff9a7fd895c1d5274527d2d4316396ee2b9
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