[med-svn] [bitseq] 08/14: delete manually created manpages (since we create them dynamically)
Andreas Tille
tille at debian.org
Sat Dec 2 08:47:47 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository bitseq.
commit 6f195ecf27839c18315cbab0c3810e8eea4242b6
Author: Andreas Tille <tille at debian.org>
Date: Wed Jan 1 21:58:32 2014 +0000
delete manually created manpages (since we create them dynamically)
---
debian/mans/convertSamples.1 | 43 -----------------
debian/mans/estimateDE.1 | 50 --------------------
debian/mans/estimateExpression.1 | 87 -----------------------------------
debian/mans/getVariance.1 | 35 --------------
debian/mans/getWithinGeneExpression.1 | 57 -----------------------
debian/mans/parseAlignment.1 | 87 -----------------------------------
debian/mans/transposeLargeFile.1 | 21 ---------
7 files changed, 380 deletions(-)
diff --git a/debian/mans/convertSamples.1 b/debian/mans/convertSamples.1
deleted file mode 100644
index 3e5c010..0000000
--- a/debian/mans/convertSamples.1
+++ /dev/null
@@ -1,43 +0,0 @@
-.TH CONVERTSAMPLES "1" "January 2014" "convertSamples 0.7.0" "User Commands"
-.SH NAME
-convertSamples \- convert or normalize MCMC expression samples
-.SH SYNOPSIS
-.B convertSamples
-\fI-a <action> -o <outFileName> \fR[\fIOPTIONS\fR] [\fIsampleFile\fR]
-.SH DESCRIPTION
-Converts or normalizes MCMC expression samples.
-.IP
-[sampleFile] should contain transposed MCMC samples.
-.SH OPTIONS
-.HP
-\fB\-\-help\fR
-.IP
-Show this help information.
-.HP
-\fB\-\-Nmap=\fR<Nmap>
-.IP
-Total number of aligned reads. Or a normalization constant, when normalizing.
-.HP
-\fB\-a\fR <action> , \fB\-\-action=\fR<action>
-.IP
-Action to perform options:
-.IP
-T2R \- theta to rpkm
-R2T \- rpkm to theta
-T2RL \- theta to log\-rpkm
-C2R \- counts to rpkm
-R2C \- rpkm 2 counts
-NORM \- normalize (samples are multiplied by Nmap)
-LOGNORM \- log+normalize (samples are multiplied by Nmap and logged).
-.HP
-\fB\-o\fR <outFileName> , \fB\-\-outFile=\fR<outFileName>
-.IP
-Name of the output file.
-.HP
-\fB\-t\fR <trInfoFileName> , \fB\-\-trInfoFile=\fR<trInfoFileName>
-.IP
-File containing transcript information.
-.HP
-\fB\-v\fR , \fB\-\-verbose\fR
-.IP
-Verbose output. (default: Off)
diff --git a/debian/mans/estimateDE.1 b/debian/mans/estimateDE.1
deleted file mode 100644
index ff82155..0000000
--- a/debian/mans/estimateDE.1
+++ /dev/null
@@ -1,50 +0,0 @@
-.TH ESTIMATEDE "1" "January 2014" "estimateDE 0.7.0" "User Commands"
-.SH NAME
-estimateDE \- this bitseq module estimates differential expression from data sets
-.SH SYNOPSIS
-.B estimateDE
-\fI\-o <outFilePrefix> \-p <parFileName> \fR[\fIOPTIONS\fR] [\fIsampleFiles\fR]
-.SH DESCRIPTION
-Estimate differential expression from the dataset.
-.IP
-[sampleFiles] should contain transposed MCMC samples from replicates.
-To distinguish conditions use C between them e.g.:
-.IP
-samplesC1\-R1.rpkm samplesC1\-R2.rpkm C samplesC2\-R1.rpkm samplesC2\-R2.rpkm
-.SH OPTIONS
-.HP
-\fB\-\-help\fR
-.IP
-Show this help information.
-.HP
-\fB\-\-confidenceInterval=\fR<cf>
-.IP
-Percentage for confidence intervals. (default: 95)
-.HP
-\fB\-l\fR <lambda0> , \fB\-\-lambda0=\fR<lambda0>
-.IP
-Parameter lambda_0. (default: 2)
-.HP
-\fB\-\-norm=\fR<normalization>
-.IP
-Normalization constants for each input file provided as comma separated list of doubles (e.g. 1.0017,1.0,0.9999 ).
-.HP
-\fB\-o\fR <outFilePrefix> , \fB\-\-outPrefix=\fR<outFilePrefix>
-.IP
-Prefix for the output files.
-.HP
-\fB\-p\fR <parFileName> , \fB\-\-parameters=\fR<parFileName>
-.IP
-File containing estimated hyperparameters.
-.HP
-\fB\-s\fR , \fB\-\-samples\fR
-.IP
-Produce samples of condition mean expression apart from PPLR and confidence. (default: Off)
-.HP
-\fB\-\-seed=\fR<seed>
-.IP
-Random initialization seed.
-.HP
-\fB\-v\fR , \fB\-\-verbose\fR
-.IP
-Verbose output. (default: Off)
diff --git a/debian/mans/estimateExpression.1 b/debian/mans/estimateExpression.1
deleted file mode 100644
index 30f8634..0000000
--- a/debian/mans/estimateExpression.1
+++ /dev/null
@@ -1,87 +0,0 @@
-.TH ESTIMATEEXPRESSION "1" "January 2014" "estimateExpression 0.7.0" "User Commands"
-.SH NAME
-estimateExpression \- estimate expression given precomputed probabilities of (observed) reads' alignments
-.SH SYNOPSIS
-.B estimateExpression
-\fI-o <outFilePrefix> \fR[\fIOPTIONS\fR] [\fIprob file\fR]
-.SH DESCRIPTION
-Estimates expression given precomputed probabilities of (observed) reads' alignments.
-.IP
-Uses MCMC sampling algorithm to produce relative abundance or RPKM.
-.SH OPTIONS
-.HP
-\fB\-\-help\fR
-.IP
-Show this help information.
-.HP
-\fB\-\-MCMC_burnIn=\fR<MCMC_burnIn>
-.IP
-Length of sampler's burn in period. (default: 1000)
-.HP
-\fB\-\-MCMC_chainsN=\fR<MCMC_chainsN>
-.IP
-Number of parallel chains used. At least two chains will be used. (default: 4)
-.HP
-\fB\-\-MCMC_dirAlpha=\fR<MCMC_dirAlpha>
-.IP
-Alpha parameter for the Dirichlet distribution. (default: 1)
-.HP
-\fB\-\-MCMC_samplesDOmax\fR
-.IP
-Produce maximum number of samples (samplesNmax) in second iteration and quit. (default: Off)
-.HP
-\fB\-\-MCMC_samplesN=\fR<MCMC_samplesN>
-.IP
-Initial number of samples produced. Doubles after every iteration. (default: 1000)
-.HP
-\fB\-\-MCMC_samplesNmax=\fR<MCMC_samplesNmax>
-.IP
-Maximum number of samples produced in one iteration. After producing samplesNmax samples sampler finishes. (default: 50000)
-.HP
-\fB\-\-MCMC_samplesSave=\fR<MCMC_samplesSave>
-.IP
-Number of samples recorder in total. (default: 1000)
-.HP
-\fB\-\-MCMC_scaleReduction=\fR<MCMC_scaleReduction>
-.IP
-Target scale reduction, sampler finishes after this value is met. (default: 1.2)
-.HP
-\fB\-G\fR , \fB\-\-gibbs\fR
-.IP
-Use Gibbs sampling instead of collapsed Gibbs sampling. (default: Off)
-.HP
-\fB\-o\fR <outFilePrefix> , \fB\-\-outPrefix=\fR<outFilePrefix>
-.IP
-Prefix for the output files.
-.HP
-\fB\-O\fR <outputType> , \fB\-\-outType=\fR<outputType>
-.IP
-Output type (theta, RPKM, counts, tau). (default: theta)
-.HP
-\fB\-p\fR <parFileName> , \fB\-\-parFile=\fR<parFileName>
-.IP
-File containing parameters for the sampler, which can be otherwise specified by \fB\-\-MCMC\fR* options. As the file is checked after every MCMC iteration, the parameters can be adjusted while running.
-.HP
-\fB\-P\fR <procN> , \fB\-\-procN=\fR<procN>
-.IP
-Limit the maximum number of threads to be used. (Default is the number of MCMC chains.)
-.HP
-\fB\-\-scaleReduction\fR
-.IP
-Use scale reduction as stopping criterion, instead of computing effective sample size. (default: Off)
-.HP
-\fB\-s\fR <seed> , \fB\-\-seed=\fR<seed>
-.IP
-Random initialization seed.
-.HP
-\fB\-\-thetaActFile=\fR<thetaActFileName>
-.IP
-File for logging noise parameter theta^{act}.
-.HP
-\fB\-t\fR <trInfoFileName> , \fB\-\-trInfoFile=\fR<trInfoFileName>
-.IP
-File containing transcript information. (Necessary for RPKM)
-.HP
-\fB\-v\fR , \fB\-\-verbose\fR
-.IP
-Verbose output. (default: Off)
diff --git a/debian/mans/getVariance.1 b/debian/mans/getVariance.1
deleted file mode 100644
index f2e5262..0000000
--- a/debian/mans/getVariance.1
+++ /dev/null
@@ -1,35 +0,0 @@
-.TH GETVARIANCE "1" "January 2014" "getVariance 0.7.0" "User Commands"
-.SH NAME
-getVariance \- estimates variance of MCMC samples
-.SH SYNOPSIS
-.B getVariance
-\fI-o <outFileName> \fR[\fIOPTIONS\fR] [\fIsampleFiles\fR]
-.SH DESCRIPTION
-Estimates variance of MCMC samples from 1 or multiple replicates.
-.IP
-[sample Files] should contain transposed MCMC samples from replicates.
-.SH OPTIONS
-.HP
-\fB\-\-help\fR
-.IP
-Show this help information.
-.HP
-\fB\-l\fR , \fB\-\-log\fR
-.IP
-Use logged values. (default: Off)
-.HP
-\fB\-\-norm=\fR<normalization>
-.IP
-Normalization constants for each input file provided as comma separated list of doubles (e.g. 1.0017,1.0,0.9999 ).
-.HP
-\fB\-o\fR <outFileName> , \fB\-\-outFile=\fR<outFileName>
-.IP
-Name of the output file.
-.HP
-\fB\-t\fR <type> , \fB\-\-type=\fR<type>
-.IP
-Type of variance, possible values: [sample,sqDif] for sample variance or squared difference. (default: sample)
-.HP
-\fB\-v\fR , \fB\-\-verbose\fR
-.IP
-Verbose output. (default: Off)
diff --git a/debian/mans/getWithinGeneExpression.1 b/debian/mans/getWithinGeneExpression.1
deleted file mode 100644
index 4375b47..0000000
--- a/debian/mans/getWithinGeneExpression.1
+++ /dev/null
@@ -1,57 +0,0 @@
-.TH GETWITHINGENEEXPRESSION "1" "January 2014" "getWithinGeneExpression 0.7.0" "User Commands"
-.SH NAME
-getWithinGeneExpression \- compute relative expression of transcripts within genes
-.SH SYNOPSIS
-.B getWithinGeneExpression
-\fI-t <trInfoFileName> \fR[\fIOPTIONS\fR] [\fIsamplesFile\fR]
-.SH DESCRIPTION
-Computes relative expression of transcripts within genes.
-.IP
-[samplesFile] should contain transposed MCMC expression samples.
-program can produce means and variance and write them into [sumFile]
-or individual MCMC samples which are written into [outFile].
-.SH OPTIONS
-.HP
-\fB\-\-help\fR
-.IP
-Show this help information.
-.HP
-\fB\-a\fR , \fB\-\-adjustByLength\fR
-.IP
-Adjust expression by transcripts length. (default: Off)
-.HP
-\fB\-G\fR <geneListFile> , \fB\-\-geneList=\fR<geneListFile>
-.IP
-Name of the file containing list of gene names (one for each transcript).
-.HP
-\fB\-\-groupByGene\fR
-.IP
-Group transcripts by genes (this can change the default order of output. (default: Off)
-.HP
-\fB\-l\fR , \fB\-\-log\fR
-.IP
-Use logged values. (default: Off)
-.HP
-\fB\-o\fR <outFileName> , \fB\-\-outFile=\fR<outFileName>
-.IP
-Name of the output file.
-.HP
-\fB\-s\fR <sumFileName> , \fB\-\-sumFile=\fR<sumFileName>
-.IP
-Name of summarization file where true mean, true variance and relative mean and relative variance are saved.
-.HP
-\fB\-t\fR <trInfoFileName> , \fB\-\-trInfoFile=\fR<trInfoFileName>
-.IP
-Name of the transcript file.
-.HP
-\fB\-T\fR <trMapFile> , \fB\-\-trMap=\fR<trMapFile>
-.IP
-Name of the file containing transcript to gene mapping.
-.HP
-\fB\-\-updateTrFile\fR
-.IP
-Update trInfoFile if new gene names were provided (with trMapFile or geneListFile). (default: Off)
-.HP
-\fB\-v\fR , \fB\-\-verbose\fR
-.IP
-Verbose output. (default: Off)
diff --git a/debian/mans/parseAlignment.1 b/debian/mans/parseAlignment.1
deleted file mode 100644
index d44c700..0000000
--- a/debian/mans/parseAlignment.1
+++ /dev/null
@@ -1,87 +0,0 @@
-.TH PARSEALIGNMENT "1" "January 2014" "parseAlignment 0.7.0" "User Commands"
-.SH NAME
-parseAlignment \- pre\-compute probabilities of (observed) reads' alignments
-.SH SYNOPSIS
-.B parseAlignment
-\fI\-o <outFileName> \-s <trSeqFileName> \-\-trSeqHeader <trSeqHeader> \fR[\fIOPTIONS\fR] [\fIalignment file\fR]
-.SH DESCRIPTION
-Pre\-computes probabilities of (observed) reads' alignments.
-.IP
-[alignment file] should be in either SAM or BAM format.
-.SH OPTIONS
-.HP
-\fB\-\-help\fR
-.IP
-Show this help information.
-.HP
-\fB\-\-distributionFile=\fR<distributionFileName>
-.IP
-Name of file to which read\-distribution should be saved.
-.HP
-\fB\-e\fR <expFileName> , \fB\-\-expressionFile=\fR<expFileName>
-.IP
-Transcript relative expression estimates \fB\-\-\-\fR for better non\-uniform read distribution estimation.
-.HP
-\fB\-\-failed=\fR<failed>
-.IP
-File name where to save names of reads that failed to align as pair.
-.HP
-\fB\-f\fR <format> , \fB\-\-format=\fR<format>
-.IP
-Input format: either SAM, BAM.
-.HP
-\fB\-\-lenMu=\fR<lenMu>
-.IP
-Set mean of log fragment length distribution. (l_frag ~ LogNormal(mu,sigma^2))
-.HP
-\fB\-\-lenSigma=\fR<lenSigma>
-.IP
-Set sigma^2 (or variance) of log fragment length distribution. (l_frag ~ LogNormal(mu,sigma^2))
-.HP
-\fB\-l\fR <maxAlignments> , \fB\-\-limitA=\fR<maxAlignments>
-.IP
-Limit maximum number of alignments per read. (Reads with more alignments are skipped.)
-.HP
-\fB\-\-noiseMismatches=\fR<numNoiseMismatches>
-.IP
-Number of mismatches to be considered as noise. (default: 6)
-.HP
-\fB\-o\fR <outFileName> , \fB\-\-outFile=\fR<outFileName>
-.IP
-Name of the output file.
-.HP
-\fB\-P\fR <procN> , \fB\-\-procN=\fR<procN>
-.IP
-Maximum number of threads to be used. This provides parallelization only when computing non\-uniform read distribution (i.e. runs without \fB\-\-uniform\fR flag). (default: 3)
-.HP
-\fB\-N\fR <readsN> , \fB\-\-readsN=\fR<readsN>
-.IP
-Total number of reads. This is not necessary if [SB]AM contains also reads with no valid alignments.
-.HP
-\fB\-t\fR <trInfoFileName> , \fB\-\-trInfoFile=\fR<trInfoFileName>
-.IP
-If transcript(reference sequence) information is contained within SAM file, program will write this information into <trInfoFile>, otherwise it will look for this information in <trInfoFile>.
-.HP
-\fB\-s\fR <trSeqFileName> , \fB\-\-trSeqFile=\fR<trSeqFileName>
-.IP
-Transcript sequence in FASTA format \fB\-\-\-\fR for non\-uniform read distribution estimation.
-.HP
-\fB\-\-trSeqHeader=\fR<trSeqHeader>
-.IP
-Transcript sequence header format enables gene name extraction (standard/gencode). (default: standard)
-.HP
-\fB\-\-uniform\fR
-.IP
-Use uniform read distribution. (default: Off)
-.HP
-\fB\-\-unstranded\fR
-.IP
-Paired read are not strand specific. (default: Off)
-.HP
-\fB\-v\fR , \fB\-\-verbose\fR
-.IP
-Verbose output. (default: Off)
-.HP
-\fB\-V\fR , \fB\-\-veryVerbose\fR
-.IP
-Very verbose output. (default: Off)
diff --git a/debian/mans/transposeLargeFile.1 b/debian/mans/transposeLargeFile.1
deleted file mode 100644
index 0c3ca3d..0000000
--- a/debian/mans/transposeLargeFile.1
+++ /dev/null
@@ -1,21 +0,0 @@
-.TH TRANSPOSELARGEFILE "1" "January 2014" "transposeLargeFile 0.7.0" "User Commands"
-.SH NAME
-transposeLargeFile \- helper for bitseq to transpose files lines and columns
-.SH SYNOPSIS
-.B transposeLargeFile
-\fI-o <outFileName> \fR[\fIOPTIONS\fR] [\fIinput files\fR]
-.SH DESCRIPTION
-Transposes [input files] into [outFileName] so that there are M lines with N columns each.
-.SH OPTIONS
-.HP
-\fB\-\-help\fR
-.IP
-Show this help information.
-.HP
-\fB\-o\fR <outFileName> , \fB\-\-outFile=\fR<outFileName>
-.IP
-Name of the output file.
-.HP
-\fB\-v\fR , \fB\-\-verbose\fR
-.IP
-Verbose output. (default: Off)
--
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