François Gindraud pushed to branch master at Debian Med / kissplice
Commits: fa5fcda8 by Francois Gindraud at 2022-04-06T14:34:54+02:00 Use CMake-installed manpage An old manpage was included in the packaging directory and overwrote the upstream one. Upstream now installs a manpage during cmake install in the correct directory. This uncompressed manpage should be compressed by dh_compress to fit the packaging guidelines. - - - - - 3 changed files: - debian/changelog - − debian/kissplice.1 - − debian/kissplice.manpages Changes: ===================================== debian/changelog ===================================== @@ -11,6 +11,7 @@ kissplice (2.6.1-1) UNRELEASED; urgency=medium * Remove gcc10 patch * Replace redirection script with symlink to bcalm * New upstream version + * Use generated doc and upsteam manpage -- Andreas Tille <[email protected]> Fri, 01 Apr 2022 11:44:54 +0200 ===================================== debian/kissplice.1 deleted ===================================== @@ -1,87 +0,0 @@ -.TH KISSPLICE "1" "June 2013" "kissplice 1.8.3-1" "User Commands" -.SH NAME -kissplice \- detection of polymorphisms in RNA-seq data. -.SH SYNOPSIS -kissplice \-h -.br -kissplice [OPTION] [\-r READFILES] -.SH DESCRIPTION -Detects alternative splicing events and other kinds of polymorphisms from -READFILES (in FASTA or FASTQ format). -.SH OPTIONS -.TP -.B -\-h, \-\-help -Show this help message and exit. -.TP -\fB\-r\fR READFILES -Input fasta/q read files (multiple, such as "\-r file1 \fB\-r\fR file2..."). -.TP -\fB\-k\fR KVAL -k\-mer size (default=25). -.TP -\fB\-l\fR LLMAX -Maximal length of the shorter path (default: 2k\-1). -.TP -\fB\-m\fR LL_MIN -Minimum length of the shorter path (default 2k\-8). -.TP -\fB\-M\fR UL_MAX -Maximum length of the longest path (default 1000), -skipped exons longer than UL_MAX are not reported. -.TP -\fB\-g\fR GRAPH_PREFIX -Path and prefix to pre\-built de Bruijn graph (suffixed -by .edges/.nodes) if jointly used with \fB\-r\fR, graph used -to find bubbles and reads used for quantification. -.TP -\fB\-o\fR OUT_DIR -Path to store the results (default = ./results). -.TP -\fB\-d\fR PATH_TO_TMP -Specific directory (absolute path) where to build -temporary files (default temporary directory otherwise). -.TP -\fB\-t\fR NBPROCS -Number of cores (must be <= number of physical cores). -.TP -\fB\-s\fR -Don't output SNPs (saves time). -.TP -\fB\-v\fR -Verbose mode. -.TP -\fB\-u\fR -Keep the nodes/edges file for unfinished bccs. -.TP -\fB\-c\fR MIN_COV -Discard k\-mers tha are present strictly less than this -number of times in the dataset. -(default 2). -.TP -\fB\-C\fR MIN_RELATIVE_COV -Discard edges with relative coverage -below MIN_RELATIVE_COV expressed as a percentage in [0,1). -(default 0.02). -.TP -\fB\-z\fR GENOME_SIZE -Estimated number of nodes in the De-Bruin Graph. -(default = 1000000000). -.TP -\fB\-e\fR MIN_EDIT_DIST -Classify as inexact repeats those bubbles whose paths' -edit distance is smaller than MIN_EDIT_DIST -(default 3). -.TP -\fB\-y\fR MAX_CYCLES -Maximal number of bubble enumerations in each bcc. If -exceeded, no bubble is output for the bcc (default -10000). -.TP -\fB\-\-timeout\fR TIMEOUT -Max amount of time (in seconds) spent for enumerating -bubbles in each bcc. If exceeded, no bubble is output -for the bcc (default 900). -.TP -\fB\-\-version\fR -Display program's version number and exit. ===================================== debian/kissplice.manpages deleted ===================================== @@ -1 +0,0 @@ -debian/kissplice.1 View it on GitLab: https://salsa.debian.org/med-team/kissplice/-/commit/fa5fcda8a8bc12468da025775532ac5af09a3613 -- View it on GitLab: https://salsa.debian.org/med-team/kissplice/-/commit/fa5fcda8a8bc12468da025775532ac5af09a3613 You're receiving this email because of your account on salsa.debian.org.
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