This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository pbsim.
commit 486bc1e1ef1cf9f83532798f847d5e5bbbccf885 Author: Sascha Steinbiss <[email protected]> Date: Thu Mar 17 11:17:49 2016 +0000 switch man page building to asciidoctor --- debian/control | 5 ++-- debian/{pbsim.1.ronn => pbsim.1.adoc} | 47 +++++++++++++++++++---------------- debian/rules | 3 +-- 3 files changed, 29 insertions(+), 26 deletions(-) diff --git a/debian/control b/debian/control index 0d14275..c62d16d 100644 --- a/debian/control +++ b/debian/control @@ -3,7 +3,8 @@ Section: science Priority: optional Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: Sascha Steinbiss <[email protected]> -Build-Depends: debhelper (>= 9), ruby-ronn +Build-Depends: debhelper (>= 9), + asciidoctor Standards-Version: 3.9.6 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/pbsim.git Vcs-Git: https://anonscm.debian.org/git/debian-med/pbsim.git @@ -18,4 +19,4 @@ Description: simulator for PacBio sequencing reads which could be useful for de novo assembly of genomes. PBSIM simulates those PacBio reads from a reference sequence by using either a model-based or sampling-based simulation. Simulated reads are useful, for example, when - developing or evaluating sequence assemblers targeted at PacBio data. \ No newline at end of file + developing or evaluating sequence assemblers targeted at PacBio data. diff --git a/debian/pbsim.1.ronn b/debian/pbsim.1.adoc similarity index 77% rename from debian/pbsim.1.ronn rename to debian/pbsim.1.adoc index 349f871..8b852e9 100644 --- a/debian/pbsim.1.ronn +++ b/debian/pbsim.1.adoc @@ -1,9 +1,12 @@ -pbsim(1) -- simulator for PacBio sequencing reads -================================================= +# pbsim(1) + +## NAME + +pbsim - simulator for PacBio sequencing reads ## SYNOPSIS -`pbsim` [options] <reference.fasta> +*pbsim* [options] <reference.fasta> ## DESCRIPTION @@ -17,61 +20,61 @@ The options for pbsim can be divided into general, sampling-based and model-base ### General options - * `--prefix`: + *--prefix*:: prefix of output files (sd). - * `--data-type`: + *--data-type*:: data type. CLR or CCS (CLR). - * `--depth`: + *--depth*:: depth of coverage (CLR: 20.0, CCS: 50.0). - * `--length-min`: + *--length-min*:: minimum length (100). - * `--length-max`: + *--length-max*:: maximum length (CLR: 25000, CCS: 2500). - * `--accuracy-min`: + *--accuracy-min*:: minimum accuracy (CLR: 0.75, CCS: fixed as 0.75). This option can be used only in case of CLR. - * `--accuracy-max`: + *--accuracy-max*:: maximum accuracy (CLR: 1.00, CCS: fixed as 1.00). This option can be used only in case of CLR. - * `--difference-ratio`: + *--difference-ratio*:: ratio of differences. substitution:insertion:deletion. Each value up to 1000 (CLR: 10:60:30, CCS:6:21:73). - * `--seed`: + *--seed*:: for a pseudorandom number generator (Unix time). ### Options for sampling-based simulation - * `--sample-fastq`: + *--sample-fastq*:: FASTQ format file to sample. - * `--sample-profile-id`: - sample-fastq (filtered) profile ID. When using `--sample-fastq`, profile is stored. `sample_profile_<ID>.fastq`, and `sample_profile_<ID>_.stats` are created. - When not using `--sample-fastq`, profile is re-used. Note that when profile is used, `--length-min,max`, `--accuracy-min,max` would be the same as the profile. + *--sample-profile-id*:: + sample-fastq (filtered) profile ID. When using *--sample-fastq*, profile is stored. `sample_profile_<ID>.fastq`, and `sample_profile_<ID>_.stats` are created. + When not using *--sample-fastq*, profile is re-used. Note that when profile is used, *--length-min,max*, *--accuracy-min,max* would be the same as the profile. ### Options for model-based simulation - * `--model_qc`: + *--model_qc*:: model of quality code. - * `--length-mean`: + *--length-mean*:: mean of length model (CLR: 3000.0, CCS:450.0). - * `--length-sd`: + *--length-sd*:: standard deviation of length model (CLR: 2300.0, CCS: 170.0). - * `--accuracy-mean`: + *--accuracy-mean*:: mean of accuracy model (CLR: 0.78, CCS: fixed as 0.98). This option can be used only in case of CLR. - * `--accuracy-sd`: + *--accuracy-sd*:: standard deviation of accuracy model (CLR: 0.02, CCS: fixed as 0.02). This option can be used only in case of CLR. @@ -115,4 +118,4 @@ pbsim is available under the terms of the GNU General Public License, version 2 ## AUTHORS -Michiaki Hamada ([email protected]), Yukiteru Ono \ No newline at end of file +Michiaki Hamada ([email protected]), Yukiteru Ono diff --git a/debian/rules b/debian/rules index ffc2581..46ca188 100755 --- a/debian/rules +++ b/debian/rules @@ -5,11 +5,10 @@ override_dh_auto_clean: rm -f debian/pbsim.1 - rm -f debian/pbsim.1.html dh_auto_clean -- override_dh_installman: - ronn debian/pbsim.1.ronn + asciidoctor -a docdate='' -b manpage debian/pbsim.1.adoc dh_installman -- override_dh_auto_install: -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/pbsim.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
