[med-svn] [spades] 03/03: remove old manpages
Sascha Steinbiss
sascha at steinbiss.name
Thu Feb 11 16:01:55 UTC 2016
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository spades.
commit df33884db73618cee76a7848623b17e38e90a62b
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Thu Feb 11 15:59:18 2016 +0000
remove old manpages
---
debian/mans/dipspades.1 | 130 ------------------------------------------------
debian/mans/spades.1 | 128 -----------------------------------------------
2 files changed, 258 deletions(-)
diff --git a/debian/mans/dipspades.1 b/debian/mans/dipspades.1
deleted file mode 100644
index c939652..0000000
--- a/debian/mans/dipspades.1
+++ /dev/null
@@ -1,130 +0,0 @@
-.TH DIPSPADES "1" "February 2014" "dipspades 3.0.0" "User Commands"
-.SH NAME
-dipspades \- genome assembler designed for diploid genomes with high heterozygosity rate
-.SH SYNOPSIS
-.B dipspades.py
-[\fIoptions\fR] \fI-o <output_dir>\fR
-.SH DESCRIPTION
-.P
-dipSPAdes: genome assembler designed for diploid genomes with high heterozygosity rate
-.P
-The dipSPAdes program belongs to the St. Petersburg genome assembler is
-intended for both standard isolates and single-cell MDA bacteria
-assemblies. It works with Illumina or IonTorrent reads and is
-capable of providing hybrid assemblies using PacBio and Sanger reads.
-You can also provide additional contigs that will be used as long
-reads.
-.SH OPTIONS
-Basic options:
-.TP
-\fB\-o\fR <output_dir>
-directory to store all the resulting files (required)
-.TP
-\fB\-\-iontorrent\fR
-this flag is required for IonTorrent data
-.TP
-\fB\-\-test\fR
-runs SPAdes on toy dataset
-.TP
-\fB\-h\fR/\-\-help
-prints this usage message
-.PP
-Input reads:
-.TP
-\fB\-\-12\fR <filename>
-file with interlaced forward and reverse paired\-end reads
-.TP
-\fB\-1\fR <filename>
-file with forward paired\-end reads
-.TP
-\fB\-2\fR <filename>
-file with reverse paired\-end reads
-.TP
-\fB\-s\fR <filename>
-file with unpaired reads
-.TP
-\fB\-\-pe\fR<#>\-12 <filename>
-file with interlaced reads for paired\-end library number <#> (<#> = 1,2,3,4,5)
-.TP
-\fB\-\-pe\fR<#>\-1 <filename>
-file with forward reads for paired\-end library number <#> (<#> = 1,2,3,4,5)
-.TP
-\fB\-\-pe\fR<#>\-2 <filename>
-file with reverse reads for paired\-end library number <#> (<#> = 1,2,3,4,5)
-.TP
-\fB\-\-pe\fR<#>\-s <filename>
-file with unpaired reads for paired\-end library number <#> (<#> = 1,2,3,4,5)
-.TP
-\fB\-\-pe\fR<#>\-<or>
-orientation of reads for paired\-end library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
-.TP
-\fB\-\-mp\fR<#>\-12 <filename>
-file with interlaced reads for mate\-pair library number <#> (<#> = 1,2,3,4,5)
-.TP
-\fB\-\-mp\fR<#>\-1 <filename>
-file with forward reads for mate\-pair library number <#> (<#> = 1,2,3,4,5)
-.TP
-\fB\-\-mp\fR<#>\-2 <filename>
-file with reverse reads for mate\-pair library number <#> (<#> = 1,2,3,4,5)
-.TP
-\fB\-\-mp\fR<#>\-s <filename>
-file with unpaired reads for mate\-pair library number <#> (<#> = 1,2,3,4,5)
-.TP
-\fB\-\-mp\fR<#>\-<or>
-orientation of reads for mate\-pair library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
-.TP
-\fB\-\-sanger\fR <filename>
-file with Sanger reads
-.TP
-\fB\-\-pacbio\fR <filename>
-file with PacBio reads
-.TP
-\fB\-\-trusted\-contigs\fR <filename>
-file with trusted contigs
-.TP
-\fB\-\-untrusted\-contigs\fR <filename>
-file with untrusted contigs
-.PP
-Input haplocontigs:
-.TP
-\fB\-\-hap\fR <filename>
-file with haplocontigs
-.PP
-Pipeline options:
-.TP
-\fB\-\-only\-assembler\fR
-runs only assembling (without read error correction)
-.TP
-\fB\-\-disable\-gzip\-output\fR
-forces error correction not to compress the corrected reads
-.TP
-\fB\-\-disable\-rr\fR
-disables repeat resolution stage of assembling
-.PP
-DipSPAdes options:
-.TP
-\fB\-\-expect\-gaps\fR
-indicate that significant number of gaps in coverage is expected
-.TP
-\fB\-\-expect\-rearrangements\fR
-indicate that significant number of rearrangngements between haplomes of diploid genome is expected
-.PP
-Advanced options:
-.TP
-\fB\-\-dataset\fR <filename>
-file with dataset description in YAML format
-.TP
-\fB\-t\fR/\-\-threads <int>
-number of threads [default: 16]
-.TP
-\fB\-m\fR/\-\-memory <int>
-RAM limit for SPAdes in Gb (terminates if exceeded) [default: 250]
-.TP
-\fB\-\-tmp\-dir\fR <dirname>
-directory for temporary files [default: <output_dir>/tmp]
-.TP
-\fB\-k\fR <int,int,...>
-comma\-separated list of k\-mer sizes (must be odd and less than 128) [default: 'auto']
-.TP
-\fB\-\-phred\-offset\fR <33 or 64>
-PHRED quality offset in the input reads (33 or 64) [default: auto\-detect]
diff --git a/debian/mans/spades.1 b/debian/mans/spades.1
deleted file mode 100644
index e65a126..0000000
--- a/debian/mans/spades.1
+++ /dev/null
@@ -1,128 +0,0 @@
-.TH SPADES "1" "February 2014" "spades 3.0.0" "User Commands"
-.SH NAME
-spades \- SPAdes genome assembler
-.SH SYNOPSIS
-.B spades.py
-[\fIoptions\fR] \fI-o <output_dir>\fR
-.SH DESCRIPTION
-The SPAdes - St. Petersburg genome assembler is intended for both
-standard isolates and single-cell MDA bacteria assemblies. It works
-with Illumina or IonTorrent reads and is capable of providing hybrid
-assemblies using PacBio and Sanger reads. You can also provide
-additional contigs that will be used as long reads.
-.SH OPTIONS
-Basic options:
-.TP
-\fB\-o\fR <output_dir>
-directory to store all the resulting files (required)
-.TP
-\fB\-\-sc\fR
-this flag is required for MDA (single\-cell) data
-.TP
-\fB\-\-iontorrent\fR
-this flag is required for IonTorrent data
-.TP
-\fB\-\-test\fR
-runs SPAdes on toy dataset
-.TP
-\fB\-h\fR/\-\-help
-prints this usage message
-.PP
-Input data:
-.TP
-\fB\-\-12\fR <filename>
-file with interlaced forward and reverse paired\-end reads
-.TP
-\fB\-1\fR <filename>
-file with forward paired\-end reads
-.TP
-\fB\-2\fR <filename>
-file with reverse paired\-end reads
-.TP
-\fB\-s\fR <filename>
-file with unpaired reads
-.TP
-\fB\-\-pe\fR<#>\-12 <filename>
-file with interlaced reads for paired\-end library number <#> (<#> = 1,2,3,4,5)
-.TP
-\fB\-\-pe\fR<#>\-1 <filename>
-file with forward reads for paired\-end library number <#> (<#> = 1,2,3,4,5)
-.TP
-\fB\-\-pe\fR<#>\-2 <filename>
-file with reverse reads for paired\-end library number <#> (<#> = 1,2,3,4,5)
-.TP
-\fB\-\-pe\fR<#>\-s <filename>
-file with unpaired reads for paired\-end library number <#> (<#> = 1,2,3,4,5)
-.TP
-\fB\-\-pe\fR<#>\-<or>
-orientation of reads for paired\-end library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
-.TP
-\fB\-\-mp\fR<#>\-12 <filename>
-file with interlaced reads for mate\-pair library number <#> (<#> = 1,2,3,4,5)
-.TP
-\fB\-\-mp\fR<#>\-1 <filename>
-file with forward reads for mate\-pair library number <#> (<#> = 1,2,3,4,5)
-.TP
-\fB\-\-mp\fR<#>\-2 <filename>
-file with reverse reads for mate\-pair library number <#> (<#> = 1,2,3,4,5)
-.TP
-\fB\-\-mp\fR<#>\-s <filename>
-file with unpaired reads for mate\-pair library number <#> (<#> = 1,2,3,4,5)
-.TP
-\fB\-\-mp\fR<#>\-<or>
-orientation of reads for mate\-pair library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
-.TP
-\fB\-\-sanger\fR <filename>
-file with Sanger reads
-.TP
-\fB\-\-pacbio\fR <filename>
-file with PacBio reads
-.TP
-\fB\-\-trusted\-contigs\fR <filename>
-file with trusted contigs
-.TP
-\fB\-\-untrusted\-contigs\fR <filename>
-file with untrusted contigs
-.PP
-Pipeline options:
-.TP
-\fB\-\-only\-error\-correction\fR
-runs only read error correction (without assembling)
-.TP
-\fB\-\-only\-assembler\fR
-runs only assembling (without read error correction)
-.TP
-\fB\-\-careful\fR
-tries to reduce number of mismatches and short indels
-.TP
-\fB\-\-continue\fR
-continue run from the last available check\-point
-.TP
-\fB\-\-restart\-from\fR <cp>
-restart run with updated options and from the specified check\-point ('ec', 'as', 'k<int>', 'mc')
-.TP
-\fB\-\-disable\-gzip\-output\fR
-forces error correction not to compress the corrected reads
-.TP
-\fB\-\-disable\-rr\fR
-disables repeat resolution stage of assembling
-.PP
-Advanced options:
-.TP
-\fB\-\-dataset\fR <filename>
-file with dataset description in YAML format
-.TP
-\fB\-t\fR/\-\-threads <int>
-number of threads [default: 16]
-.TP
-\fB\-m\fR/\-\-memory <int>
-RAM limit for SPAdes in Gb (terminates if exceeded) [default: 250]
-.TP
-\fB\-\-tmp\-dir\fR <dirname>
-directory for temporary files [default: <output_dir>/tmp]
-.TP
-\fB\-k\fR <int,int,...>
-comma\-separated list of k\-mer sizes (must be odd and less than 128) [default: 'auto']
-.TP
-\fB\-\-phred\-offset\fR <33 or 64>
-PHRED quality offset in the input reads (33 or 64) [default: auto\-detect]
--
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