update doc

Makefile.am

@@ -87,7 +87,7 @@ clean-local: clean-local-check
 clean-local-check:
 	-rm -rf src/*.gc* tests/unittest/*.gc* src/*.gcov
 
-utilities: utilities/dataExplore.r utilities/interpretDEploid.r
+utilities_SOURCES = utilities/dataExplore.r utilities/interpretDEploid.r
+utilities:
 	sed -i'.bak' -e '/#!\/usr\/bin\/env Rscript/d' -e '/rm(list=ls())/d' utilities/dataExplore.r ; echo "#!/usr/bin/env Rscript" > tmpTxt; echo "rm(list=ls()); dEploidRootDir=\"$(PWD)\"" >> tmpTxt ; cat utilities/dataExplore.r >> tmpTxt ; mv tmpTxt utilities/dataExplore.r; chmod a+x utilities/dataExplore.r;
 	sed -i'.bak' -e '/#!\/usr\/bin\/env Rscript/d' -e '/rm(list=ls())/d' utilities/interpretDEploid.r; echo "#!/usr/bin/env Rscript" > tmpTxt; echo "rm(list=ls()); dEploidRootDir=\"$(PWD)\"" >> tmpTxt ; cat utilities/interpretDEploid.r >> tmpTxt ; mv tmpTxt utilities/interpretDEploid.r; chmod a+x utilities/interpretDEploid.r
-

configure.ac

@@ -16,6 +16,7 @@ AM_SILENT_RULES([yes])
 AC_PROG_INSTALL
 AC_PREREQ
 AC_CANONICAL_HOST
+AC_PROG_F77
 
 # Checks for programs.
 AC_PROG_RANLIB

docs/Output.md

@@ -31,8 +31,17 @@ When flag ``-vcfOut`` is turned on, haplotypes are saved at the final iteration
 
 When flag ``-exportPostProb`` is turned on, posterior probabilities of the final iteration of strain [i].
 
+### DEploid-IBD
 
-Example of output interpretion
+When "flag" ``-ibd`` is used. 'DEploid' executes first learns the number of strain and their proportions with an identity by descent model ('DEploid-IBD'). Then it fixes the number of strains and proportions and train the haplotypes, and train the haplotypes using the original DEploid algorithm ('DEploid-classic'). The staged output are labelled with ".ibd" and ".classic" respectively, and followed by the prefix.
+
+
+### DEploid-BEST
+
+When "flag" ``-best`` is used. 'DEploid-BEST' executes the deconvolution algorithms in an optimised sequence to best report the number of strains, proportions and haplotypes. The program ('DEploid-Lasso') learns the number of strain with optimised reference panel; ".chooseK" is appended to the prefix for these output (NOTE: likelihood is not tracked in this case). It ('DEploid-IBD') then fixes the number of strains and tune the strain proportions with an identity by descent model; ".ibd" is appended to the prefix for these output. Finally, the program ('DEploid-Lasso') fixes the number of strains and proportions, and uses the optimised reference panel again to train and report the haplotypes; ".final" is appended to the prefix for these output. When  ``-vcfOut`` and ``-exportPostProb`` are applied, these outputs will only associate with the final haplotypes.
+
+
+Example of output interpretation
 ------------------------------
 
 ### Example 1. Standard deconvolution output

docs/_build/man/dEploid.1

@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "DEPLOID" "1" "Nov 03, 2019" "v0.6-beta" "DEploid"
+.TH "DEPLOID" "1" "Nov 16, 2019" "v0.6-beta" "DEploid"
 .SH NAME
 dEploid \- 
 .
@@ -559,48 +559,62 @@ Figure on the right show allele frequency within sample, compare against the pop
 .SS Output files
 .sp
 \fBdEploid\fP outputs text files with user\-specified prefix with flag \fB\-o\fP\&.
-.INDENT 0.0
-.TP
-.B \fIprefix\fP\&.log
+.sp
+\fB\fIprefix\fP\fP\fB\&.log\fP
+.sp
 Log file records \fBdEploid\fP version, input file paths, parameter used and proportion estimates at the final iteration.
-.TP
-.B \fIprefix\fP\&.llk
+.sp
+\fB\fIprefix\fP\fP\fB\&.llk\fP
+.sp
 Log likelihood of the MCMC chain.
-.TP
-.B \fIprefix\fP\&.prop
+.sp
+\fB\fIprefix\fP\fP\fB\&.prop\fP
+.sp
 MCMC updates of the proportion estimates.
-.TP
-.B \fIprefix\fP\&.hap
+.sp
+\fB\fIprefix\fP\fP\fB\&.hap\fP
+.sp
 Haplotypes at the final iteration in plain text file.
-.TP
-.B \fIprefix\fP\&.vcf
+.sp
+\fB\fIprefix\fP\fP\fB\&.vcf\fP
+.sp
 When flag \fB\-vcfOut\fP is turned on, haplotypes are saved at the final iteration in VCF format.
-.TP
-.B \fIprefix\fP\&.single[i]
-When flag \fB\-exportPostProb\fP is turned on, posterior probabilities of the final iteration of strain [i].
-.UNINDENT
-.SS Example of output interpretion
+.sp
+\fB\fIprefix\fP\fP\fB\&.single[i]\fP
+.sp
+When flag \fB\-exportPostProb\fP is turned on, posterior probabilities of the final iteration of strain [i]\&.
+.SS DEploid\-IBD
+.sp
+When "flag" \fB\-ibd\fP is used. \(aqDEploid\(aq executes first learns the number of strain and their proportions with an identity by descent model (\(aqDEploid\-IBD\(aq). Then it fixes the number of strains and proportions and train the haplotypes, and train the haplotypes using the original DEploid algorithm (\(aqDEploid\-classic\(aq). The staged output are labelled with ".ibd" and ".classic" respectively, and followed by the prefix.
+.SS DEploid\-BEST
+.sp
+When "flag" \fB\-best\fP is used. \(aqDEploid\-BEST\(aq executes the deconvolution algorithms in an optimised sequence to best report the number of strains, proportions and haplotypes. The program (\(aqDEploid\-Lasso\(aq) learns the number of strain with optimised reference panel; ".chooseK" is appended to the prefix for these output (NOTE: likelihood is not tracked in this case). It (\(aqDEploid\-IBD\(aq) then fixes the number of strains and tune the strain proportions with an identity by descent model; ".ibd" is appended to the prefix for these output. Finally, the program (\(aqDEploid\-Lasso\(aq) fixes the number of strains and proportions, and uses the optimised reference panel again to train and report the haplotypes; ".final" is appended to the prefix for these output. When  \fB\-vcfOut\fP and \fB\-exportPostProb\fP are applied, these outputs will only associate with the final haplotypes.
+.SS Example of output interpretation
 .SS Example 1. Standard deconvolution output
 .INDENT 0.0
 .INDENT 3.5
 .sp
 .nf
 .ft C
-$ ./dEploid \-vcf data/exampleData/PG0390\-C.eg.vcf.gz \e
-\-plaf data/exampleData/labStrains.eg.PLAF.txt \e
-\-noPanel \-o PG0390\-CNopanel \-seed 1
-$ utilities/interpretDEploid.r \-vcf data/exampleData/PG0390\-C.eg.vcf.gz \e
-\-plaf data/exampleData/labStrains.eg.PLAF.txt \e
-\-dEprefix PG0390\-CNopanel \e
-\-o PG0390\-CNopanel \-ring
+    $ ./dEploid \-vcf data/exampleData/PG0390\-C.eg.vcf.gz \e
+    \-plaf data/exampleData/labStrains.eg.PLAF.txt \e
+    \-noPanel \-o PG0390\-CNopanel \-seed 1
+    $ utilities/interpretDEploid.r \-vcf data/exampleData/PG0390\-C.eg.vcf.gz \e
+    \-plaf data/exampleData/labStrains.eg.PLAF.txt \e
+    \-dEprefix PG0390\-CNopanel \e
+    \-o PG0390\-CNopanel \-ring
+
+
 .ft P
 .fi
 .UNINDENT
 .UNINDENT
+.sp
 [image: interpretDEploidFigure.1]
 [image]
+
 .sp
-The top three figures are the same as figures show in data example, with a small addition of inferred WSAF marked in blue, in the top right figure.
+The top three figures are the same as figures show in :ref:\fBdata example <sec\-eg>\fP, with a small addition of inferred WSAF marked in blue, in the top right figure.
 .INDENT 0.0
 .IP \(bu 2
 The bottom left figure show the relative proportion change history of the MCMC chain.
@@ -609,8 +623,10 @@ The middle figure show the correlation between the expected and observed allele
 .IP \(bu 2
 The right figure shows changes in MCMC likelihood .
 .UNINDENT
+.sp
 [image: interpretDEploidFigure.2]
 [image]
+
 .sp
 This panel figure shows all allele frequencies within sample across all 14 chromosomes. Expected and observed WSAF are marked in blue and red respectively.
 .SS Example 2. Haplotype painting from a given panel
@@ -621,31 +637,37 @@ This panel figure shows all allele frequencies within sample across all 14 chrom
 .sp
 .nf
 .ft C
-$ ./dEploid \-vcf data/exampleData/PG0390\-C.eg.vcf.gz \e
-\-plaf data/exampleData/labStrains.eg.PLAF.txt \e
-\-panel data/exampleData/labStrains.eg.panel.txt \e
-\-o PG0390\-CPanel \-seed 1 \-k 3
-$ ./dEploid \-vcf data/exampleData/PG0390\-C.eg.vcf.gz \e
-\-plaf data/exampleData/labStrains.eg.PLAF.txt \e
-\-panel data/exampleData/labStrains.eg.panel.txt \e
-\-o PG0390\-CPanel \e
-\-painting PG0390\-CPanel.hap \e
-\-initialP 0.8 0 0.2 \-k 3
-$ utilities/interpretDEploid.r \-vcf data/exampleData/PG0390\-C.eg.vcf.gz \e
-\-plaf data/exampleData/labStrains.eg.PLAF.txt \e
-\-dEprefix PG0390\-CPanel \e
-\-o PG0390\-CPanel \-ring
+    $ ./dEploid \-vcf data/exampleData/PG0390\-C.eg.vcf.gz \e
+    \-plaf data/exampleData/labStrains.eg.PLAF.txt \e
+    \-panel data/exampleData/labStrains.eg.panel.txt \e
+    \-o PG0390\-CPanel \-seed 1 \-k 3
+    $ ./dEploid \-vcf data/exampleData/PG0390\-C.eg.vcf.gz \e
+    \-plaf data/exampleData/labStrains.eg.PLAF.txt \e
+    \-panel data/exampleData/labStrains.eg.panel.txt \e
+    \-o PG0390\-CPanel \e
+    \-painting PG0390\-CPanel.hap \e
+    \-initialP 0.8 0 0.2 \-k 3
+    $ utilities/interpretDEploid.r \-vcf data/exampleData/PG0390\-C.eg.vcf.gz \e
+    \-plaf data/exampleData/labStrains.eg.PLAF.txt \e
+    \-dEprefix PG0390\-CPanel \e
+    \-o PG0390\-CPanel \-ring
+
+
 .ft P
 .fi
 .UNINDENT
 .UNINDENT
+.sp
 [image: PG0390fwdBwdRing]
 [image]
+
 .SS Example 3. Deconvolution followed by IBD painting
 .sp
 In addition to lab mixed samples, here we show example of \fBdEploid\fP deconvolute field sample PD0577\-C.
+.sp
 [image: PD0577inbreeding]
 [image]
+
 .SH PF3K WORKFLOW
 .sp
 Our main work flow consist with three steps: