[med-svn] [Git][med-team/cutesv][master] Fairly happy.
Steffen Möller (@moeller)
gitlab at salsa.debian.org
Mon Jul 19 15:22:43 BST 2021
Steffen Möller pushed to branch master at Debian Med / cutesv
Commits:
c6e16984 by Steffen Moeller at 2021-07-19T16:21:53+02:00
Fairly happy.
- - - - -
9 changed files:
- + debian/README.source
- debian/changelog
- debian/control
- + debian/createmanpages
- + debian/cuteSV.1
- + debian/manpages
- + debian/patches/PythonPath.patch
- + debian/patches/series
- debian/rules
Changes:
=====================================
debian/README.source
=====================================
@@ -0,0 +1,5 @@
+The file debian/cuteSV.1 was created by the script debian/createmanpages,
+which again depends on help2man. That dependency was not formally stated
+in d/control.
+
+ -- Steffen Moeller <moeller at debian.org> Mon, 19 Jul 2021 15:50:30 +0200
=====================================
debian/changelog
=====================================
@@ -1,5 +1,5 @@
cutesv (1.0.11-1) UNRELEASED; urgency=medium
- * Initial release (Closes: #<bug>)
+ * Initial release (Closes: #991277)
-- Andreas Tille <tille at debian.org> Sat, 22 May 2021 08:48:12 +0200
=====================================
debian/control
=====================================
@@ -1,6 +1,7 @@
Source: cutesv
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+ Steffen Moeller <moeller at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
@@ -17,13 +18,15 @@ Package: cutesv
Architecture: all
Depends: ${python3:Depends},
${misc:Depends},
- python3-cigar
+ python3-cigar,
+ python3-vcf
Description: comprehensive discovery of structural variations of genomic sequences
Long-read sequencing enables the comprehensive discovery of structural
variations (SVs). However, it is still non-trivial to achieve high
sensitivity and performance simultaneously due to the complex SV
- characteristics implied by noisy long reads. Therefore, we propose
- cuteSV, a sensitive, fast and scalable long-read-based SV detection
+ characteristics implied by noisy long reads.
+ .
+ cuteSV is a sensitive, fast and scalable long-read-based SV detection
approach. cuteSV uses tailored methods to collect the signatures of
various types of SVs and employs a clustering-and-refinement method to
analyze the signatures to implement sensitive SV detection. Benchmarks
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,5 @@
+#!/bin/bash
+PYTHONPATH=src \
+ help2man --no-info -n "prediction of structural variants from sequence alignments" \
+ -s 1 --no-discard-stderr -o debian/cuteSV.1 \
+ "python3 src/cuteSV/cuteSV"
=====================================
debian/cuteSV.1
=====================================
@@ -0,0 +1,198 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.48.3.
+.TH CUTESV "1" "July 2021" "cuteSV 1.0.11" "User Commands"
+.SH NAME
+cuteSV \- prediction of structural variants from sequence alignments
+.SH DESCRIPTION
+usage: cuteSV [\-h] [\-\-version] [\-t THREADS] [\-b BATCHES] [\-S SAMPLE]
+.IP
+[\-\-retain_work_dir] [\-\-report_readid] [\-p MAX_SPLIT_PARTS]
+[\-q MIN_MAPQ] [\-r MIN_READ_LEN] [\-md MERGE_DEL_THRESHOLD]
+[\-mi MERGE_INS_THRESHOLD] [\-s MIN_SUPPORT] [\-l MIN_SIZE]
+[\-L MAX_SIZE] [\-sl MIN_SIGLENGTH] [\-\-genotype]
+[\-\-gt_round GT_ROUND] [\-Ivcf IVCF]
+[\-\-max_cluster_bias_INS MAX_CLUSTER_BIAS_INS]
+[\-\-diff_ratio_merging_INS DIFF_RATIO_MERGING_INS]
+[\-\-max_cluster_bias_DEL MAX_CLUSTER_BIAS_DEL]
+[\-\-diff_ratio_merging_DEL DIFF_RATIO_MERGING_DEL]
+[\-\-max_cluster_bias_INV MAX_CLUSTER_BIAS_INV]
+[\-\-max_cluster_bias_DUP MAX_CLUSTER_BIAS_DUP]
+[\-\-max_cluster_bias_TRA MAX_CLUSTER_BIAS_TRA]
+[\-\-diff_ratio_filtering_TRA DIFF_RATIO_FILTERING_TRA]
+[BAM] reference output work_dir
+.PP
+
+.IP
+Current version: v1.0.11
+Author: Tao Jiang
+Contact: tjiang at hit.edu.cn
+.IP
+If you use cuteSV in your work, please cite:
+.IP
+Jiang T et al. Long\-read\-based human genomic structural variation detection with cuteSV.
+Genome Biol 21,189(2020). https://doi.org/10.1186/s13059\-020\-02107\-y
+.IP
+Suggestions:
+.IP
+For PacBio CLR data:
+.TP
+\fB\-\-max_cluster_bias_INS\fR
+100
+.TP
+\fB\-\-diff_ratio_merging_INS\fR
+0.3
+.TP
+\fB\-\-max_cluster_bias_DEL\fR
+200
+.TP
+\fB\-\-diff_ratio_merging_DEL\fR
+0.5
+.IP
+For PacBio CCS(HIFI) data:
+.TP
+\fB\-\-max_cluster_bias_INS\fR
+1000
+.TP
+\fB\-\-diff_ratio_merging_INS\fR
+0.9
+.TP
+\fB\-\-max_cluster_bias_DEL\fR
+1000
+.TP
+\fB\-\-diff_ratio_merging_DEL\fR
+0.5
+.IP
+For ONT data:
+.TP
+\fB\-\-max_cluster_bias_INS\fR
+100
+.TP
+\fB\-\-diff_ratio_merging_INS\fR
+0.3
+.TP
+\fB\-\-max_cluster_bias_DEL\fR
+100
+.TP
+\fB\-\-diff_ratio_merging_DEL\fR
+0.3
+.PP
+
+.SS "positional arguments:"
+.TP
+[BAM]
+Sorted .bam file form NGMLR or Minimap2.
+.TP
+reference
+The reference genome in fasta format.
+.TP
+output
+Output VCF format file.
+.TP
+work_dir
+Work\-directory for distributed jobs
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-version\fR, \fB\-v\fR
+show program's version number and exit
+.TP
+\fB\-t\fR THREADS, \fB\-\-threads\fR THREADS
+Number of threads to use.[16]
+.TP
+\fB\-b\fR BATCHES, \fB\-\-batches\fR BATCHES
+Batch of genome segmentation interval.[10000000]
+.TP
+\fB\-S\fR SAMPLE, \fB\-\-sample\fR SAMPLE
+Sample name/id
+.TP
+\fB\-\-retain_work_dir\fR
+Enable to retain temporary folder and files.
+.TP
+\fB\-\-report_readid\fR
+Enable to report supporting read ids for each SV.
+.SS "Collection of SV signatures:"
+.TP
+\fB\-p\fR MAX_SPLIT_PARTS, \fB\-\-max_split_parts\fR MAX_SPLIT_PARTS
+Maximum number of split segments a read may be aligned
+before it is ignored. All split segments are
+considered when using \fB\-1\fR. (Recommand \fB\-1\fR when applying
+assembly\-based alignment.)[7]
+.TP
+\fB\-q\fR MIN_MAPQ, \fB\-\-min_mapq\fR MIN_MAPQ
+Minimum mapping quality value of alignment to be taken
+into account.[20]
+.TP
+\fB\-r\fR MIN_READ_LEN, \fB\-\-min_read_len\fR MIN_READ_LEN
+Ignores reads that only report alignments with not
+longer than bp.[500]
+.TP
+\fB\-md\fR MERGE_DEL_THRESHOLD, \fB\-\-merge_del_threshold\fR MERGE_DEL_THRESHOLD
+Maximum distance of deletion signals to be merged. In
+our paper, I used \fB\-md\fR 500 to process HG002 real human
+sample data.[0]
+.TP
+\fB\-mi\fR MERGE_INS_THRESHOLD, \fB\-\-merge_ins_threshold\fR MERGE_INS_THRESHOLD
+Maximum distance of insertion signals to be merged. In
+our paper, I used \fB\-mi\fR 500 to process HG002 real human
+sample data.[100]
+.SS "Generation of SV clusters:"
+.TP
+\fB\-s\fR MIN_SUPPORT, \fB\-\-min_support\fR MIN_SUPPORT
+Minimum number of reads that support a SV to be
+reported.[10]
+.TP
+\fB\-l\fR MIN_SIZE, \fB\-\-min_size\fR MIN_SIZE
+Minimum size of SV to be reported.[30]
+.TP
+\fB\-L\fR MAX_SIZE, \fB\-\-max_size\fR MAX_SIZE
+Maximum size of SV to be reported.[100000]
+.TP
+\fB\-sl\fR MIN_SIGLENGTH, \fB\-\-min_siglength\fR MIN_SIGLENGTH
+Minimum length of SV signal to be extracted.[10]
+.SS "Computing genotypes:"
+.TP
+\fB\-\-genotype\fR
+Enable to generate genotypes.
+.TP
+\fB\-\-gt_round\fR GT_ROUND
+Maximum round of iteration for alignments searching if
+perform genotyping.[500]
+.SS "Force calling:"
+.TP
+\fB\-Ivcf\fR IVCF
+Optional given vcf file. Enable to perform force
+calling. [NULL]
+.SS "Advanced:"
+.TP
+\fB\-\-max_cluster_bias_INS\fR MAX_CLUSTER_BIAS_INS
+Maximum distance to cluster read together for
+insertion.[100]
+.TP
+\fB\-\-diff_ratio_merging_INS\fR DIFF_RATIO_MERGING_INS
+Do not merge breakpoints with basepair identity more
+than [0.3] for insertion.
+.TP
+\fB\-\-max_cluster_bias_DEL\fR MAX_CLUSTER_BIAS_DEL
+Maximum distance to cluster read together for
+deletion.[200]
+.TP
+\fB\-\-diff_ratio_merging_DEL\fR DIFF_RATIO_MERGING_DEL
+Do not merge breakpoints with basepair identity more
+than [0.5] for deletion.
+.TP
+\fB\-\-max_cluster_bias_INV\fR MAX_CLUSTER_BIAS_INV
+Maximum distance to cluster read together for
+inversion.[500]
+.TP
+\fB\-\-max_cluster_bias_DUP\fR MAX_CLUSTER_BIAS_DUP
+Maximum distance to cluster read together for
+duplication.[500]
+.TP
+\fB\-\-max_cluster_bias_TRA\fR MAX_CLUSTER_BIAS_TRA
+Maximum distance to cluster read together for
+translocation.[50]
+.TP
+\fB\-\-diff_ratio_filtering_TRA\fR DIFF_RATIO_FILTERING_TRA
+Filter breakpoints with basepair identity less than
+[0.6] for translocation.
=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/cuteSV.1
=====================================
debian/patches/PythonPath.patch
=====================================
@@ -0,0 +1,10 @@
+Index: cutesv/src/cuteSV/cuteSV
+===================================================================
+--- cutesv.orig/src/cuteSV/cuteSV
++++ cutesv/src/cuteSV/cuteSV
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ '''
+ * All rights Reserved, Designed By HIT-Bioinformatics
=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+PythonPath.patch
=====================================
debian/rules
=====================================
@@ -1,6 +1,6 @@
#!/usr/bin/make -f
-# DH_VERBOSE := 1
+DH_VERBOSE := 1
%:
dh $@ --with python3 --buildsystem=pybuild
@@ -9,6 +9,10 @@ override_dh_install:
dh_install
find debian -name LICENSE -delete
+override_dh_auto_clean:
+ dh_auto_clean
+ rm -rf src/cuteSV.egg-info
+
### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
#override_dh_auto_test:
#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
View it on GitLab: https://salsa.debian.org/med-team/cutesv/-/commit/c6e169841ecae52e73aba469874daa26766c34f4
--
View it on GitLab: https://salsa.debian.org/med-team/cutesv/-/commit/c6e169841ecae52e73aba469874daa26766c34f4
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