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commit f482fd72c2701d1926bb7ce9ce5e5e1921bff3aa
Author: Steffen Moeller <moel...@debian.org>
Date:   Tue Aug 8 02:25:42 2017 +0200

    Review for adding registry references
---
 debian/changelog                               | 13 +++++
 debian/control                                 | 29 ++++++----
 debian/copyright                               |  2 +-
 debian/createmanpages                          |  9 ++-
 debian/{idba_hybrid.1 => idba.1}               | 43 +++-----------
 debian/idba.dirs                               |  1 +
 debian/idba_hybrid.1                           | 17 ++----
 debian/idba_tran.1                             | 79 ++++++++++++++++++++++++++
 debian/{idba_hybrid.1 => idba_ud.1}            | 31 +++-------
 debian/links                                   |  2 -
 debian/manpages                                |  5 +-
 debian/patches/install_all_idba_flavours.patch | 28 +++++++++
 debian/patches/series                          |  1 +
 debian/rules                                   |  4 +-
 debian/upstream/metadata                       | 44 ++++++++++----
 15 files changed, 210 insertions(+), 98 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index d252a37..ecc141d 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,16 @@
+idba (1.1.3-2) unstable; urgency=medium
+
+  * Team upload.
+
+  * Install all IDBA flavours, not only IDBA-Hybrid
+    - added help2man-generated man pages
+    - removed debian/links to save idba binary and .1
+  * Moved peripheral binaries to new dir usr/lib/idba/
+  * Added references to OMICtools registry
+  * Bumped Debian policy compliance to 4.0.1
+
+ -- Steffen Moeller <moel...@debian.org>  Mon, 07 Aug 2017 17:40:39 +0200
+
 idba (1.1.3-1) unstable; urgency=medium
 
   * New upstream version
diff --git a/debian/control b/debian/control
index c6b741e..6ba53a2 100644
--- a/debian/control
+++ b/debian/control
@@ -5,7 +5,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper (>= 9),
                dh-autoreconf
-Standards-Version: 3.9.8
+Standards-Version: 4.0.1
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/idba.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/idba.git
 Homepage: https://github.com/loneknightpy/idba
@@ -15,12 +15,21 @@ Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
          python
-Description: iterative De Bruijn Graph De Novo short read assembler for 
transcriptome
- IDBA-Tran is an iterative De Bruijn Graph De Novo short read assembler
- for transcriptome. It is purely de novo assembler based on only RNA
- sequencing reads. IDBA-Tran uses local assembly to reconstructing
- missing k-mers in low-expressed transcripts and then employs progressive
- cutoff on contigs to separate the graph into components. Each component
- corresponds to one gene in most cases and contains not many transcripts.
- A heuristic algorithm based on pair-end reads is then used to find the
- isoforms. 
+Description: iterative De Bruijn Graph short read assemblers
+ IDBA stands for iterative de Bruijn graph assembler. In computational
+ sequence biology, an assembler solves the puzzle coming from large
+ sequencing machines that feature many gigabytes of short reads from a
+ large genome.
+ .
+ This package provides several flavours of the IDBA assembler, as they all
+ share the same source tree but serve different purposes and evolved over time.
+ .
+ IDBA is the basic iterative de Bruijn graph assembler for
+ second-generation sequencing reads. IDBA-UD, an extension of IDBA,
+ is designed to utilize paired-end reads to assemble low-depth regions
+ and use progressive depth on contigs to reduce errors in high-depth
+ regions. It is a generic purpose assembler and especially good for
+ single-cell and metagenomic sequencing data. IDBA-Hybrid is another
+ update version of IDBA-UD, which can make use of a similar reference
+ genome to improve assembly result. IDBA-Tran is an iterative de Bruijn
+ graph assembler for RNA-Seq data.
diff --git a/debian/copyright b/debian/copyright
index f9cec80..dffc420 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,5 +1,5 @@
 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: IDBA-Tran
+Upstream-Name: IDBA-Tran and IDBA-UD and IDBA and IDBA-Hybrid
 Upstream-Contact: Yu Peng <yp...@cs.hku.hk>
 Source: https://github.com/loneknightpy/idba
 
diff --git a/debian/createmanpages b/debian/createmanpages
index 9c8dff8..f21e93b 100755
--- a/debian/createmanpages
+++ b/debian/createmanpages
@@ -2,6 +2,9 @@
 VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 
's/^[0-9]*://' -e 's/-.*//'`
 MANDIR=debian
 mkdir -p $MANDIR
-help2man --no-info --no-discard-stderr \
-         --name='Iterative de Bruijn Graph Assembler for hybrid sequencing 
data' \
-            --version-string="$VERSION" idba_hybrid > $MANDIR/idba_hybrid.1
+for i in idba idba_tran idba_hybrid idba_ud
+do
+  help2man --no-info --no-discard-stderr \
+           --name='Iterative de Bruijn Graph Assembler for hybrid sequencing 
data' \
+           --version-string="$VERSION" bin/$i | grep -v "unknown option" | 
grep -v "bin/idba" > $MANDIR/$i.1
+done
diff --git a/debian/idba_hybrid.1 b/debian/idba.1
similarity index 54%
copy from debian/idba_hybrid.1
copy to debian/idba.1
index 9f0b69e..fbb0646 100644
--- a/debian/idba_hybrid.1
+++ b/debian/idba.1
@@ -1,20 +1,13 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.43.3.
-.TH IDBA_HYBRID "1" "February 2014" "idba_hybrid 1.1.1" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
+.TH IDBA "1" "August 2017" "idba 1.1.3" "User Commands"
 .SH NAME
-idba_hybrid \- Iterative de Bruijn Graph Assembler for hybrid sequencing data
+idba \- Iterative de Bruijn Graph Assembler for hybrid sequencing data
 .SH SYNOPSIS
-.B idba_hybrid
-\fI\-r read.fa \-o output_dir \fR[\fI\-\-reference ref.fa\fR]
+.B idba_ud
+\fI\,-r read.fa -o output_dir\/\fR
 .SH DESCRIPTION
-IDBA-Tran is an iterative De Bruijn Graph De Novo short read assembler
-for transcriptome. It is purely de novo assembler based on only RNA
-sequencing reads. IDBA-Tran uses local assembly to reconstructing
-missing k-mers in low-expressed transcripts and then employs progressive
-cutoff on contigs to separate the graph into components. Each component
-corresponds to one gene in most cases and contains not many transcripts.
-A heuristic algorithm based on pair-end reads is then used to find the
-isoforms.
-.SH OPTIONS
+IDBA\- Iterative de Bruijn Graph Assembler.
+.SS "Allowed Options:"
 .TP
 \fB\-o\fR, \fB\-\-out\fR arg (=out)
 output directory
@@ -37,24 +30,15 @@ paired\-end reads fasta for fifth level scaffolds
 \fB\-l\fR, \fB\-\-long_read\fR arg
 fasta long read file (>128)
 .TP
-\fB\-\-reference\fR arg
-reference genome
-.TP
 \fB\-\-mink\fR arg (=20)
 minimum k value (<=124)
 .TP
-\fB\-\-maxk\fR arg (=100)
+\fB\-\-maxk\fR arg (=50)
 maximum k value (<=124)
 .TP
-\fB\-\-step\fR arg (=20)
+\fB\-\-step\fR arg (=10)
 increment of k\-mer of each iteration
 .TP
-\fB\-\-inner_mink\fR arg (=10)
-inner minimum k value
-.TP
-\fB\-\-inner_step\fR arg (=5)
-inner increment of k\-mer
-.TP
 \fB\-\-prefix\fR arg (=3)
 prefix length used to build sub k\-mer table
 .TP
@@ -73,9 +57,6 @@ seed kmer size for alignment
 \fB\-\-min_contig\fR arg (=200)
 minimum size of contig
 .TP
-\fB\-\-min_region\fR arg (=500)
-minimum size of region in reference genome
-.TP
 \fB\-\-similar\fR arg (=0.95)
 similarity for alignment
 .TP
@@ -85,12 +66,6 @@ max mismatch of error correction
 \fB\-\-min_pairs\fR arg (=3)
 minimum number of pairs
 .TP
-\fB\-\-max_gap\fR arg (=50)
-maximum gap in reference
-.TP
-\fB\-\-no_local\fR
-do not use local assembly
-.TP
 \fB\-\-no_coverage\fR
 do not iterate on coverage
 .TP
diff --git a/debian/idba.dirs b/debian/idba.dirs
new file mode 100644
index 0000000..dc523cf
--- /dev/null
+++ b/debian/idba.dirs
@@ -0,0 +1 @@
+usr/lib/idba
diff --git a/debian/idba_hybrid.1 b/debian/idba_hybrid.1
index 9f0b69e..b002347 100644
--- a/debian/idba_hybrid.1
+++ b/debian/idba_hybrid.1
@@ -1,20 +1,13 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.43.3.
-.TH IDBA_HYBRID "1" "February 2014" "idba_hybrid 1.1.1" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
+.TH IDBA_HYBRID "1" "August 2017" "idba_hybrid 1.1.3" "User Commands"
 .SH NAME
 idba_hybrid \- Iterative de Bruijn Graph Assembler for hybrid sequencing data
 .SH SYNOPSIS
 .B idba_hybrid
-\fI\-r read.fa \-o output_dir \fR[\fI\-\-reference ref.fa\fR]
+\fI\,-r read.fa -o output_dir \/\fR[\fI\,--reference ref.fa\/\fR]
 .SH DESCRIPTION
-IDBA-Tran is an iterative De Bruijn Graph De Novo short read assembler
-for transcriptome. It is purely de novo assembler based on only RNA
-sequencing reads. IDBA-Tran uses local assembly to reconstructing
-missing k-mers in low-expressed transcripts and then employs progressive
-cutoff on contigs to separate the graph into components. Each component
-corresponds to one gene in most cases and contains not many transcripts.
-A heuristic algorithm based on pair-end reads is then used to find the
-isoforms.
-.SH OPTIONS
+IDBA\-Hybrid \- Iterative de Bruijn Graph Assembler for hybrid sequencing data.
+.SS "Allowed Options:"
 .TP
 \fB\-o\fR, \fB\-\-out\fR arg (=out)
 output directory
diff --git a/debian/idba_tran.1 b/debian/idba_tran.1
new file mode 100644
index 0000000..9512e86
--- /dev/null
+++ b/debian/idba_tran.1
@@ -0,0 +1,79 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
+.TH IDBA_TRAN "1" "August 2017" "idba_tran 1.1.3" "User Commands"
+.SH NAME
+idba_tran \- Iterative de Bruijn Graph Assembler for hybrid sequencing data
+.SH SYNOPSIS
+.B idba_tran
+\fI\,-r read.fa -o output_dir\/\fR
+.SH DESCRIPTION
+IDBA\-Tran \- Iterative de Bruijn Graph Assembler for next\-generation 
transcriptome sequencing data.
+.SS "Allowed Options:"
+.TP
+\fB\-o\fR, \fB\-\-out\fR arg (=out)
+output directory
+.TP
+\fB\-r\fR, \fB\-\-read\fR arg
+fasta read file (<=128)
+.TP
+\fB\-l\fR, \fB\-\-long_read\fR arg
+fasta long read file (>128)
+.TP
+\fB\-\-mink\fR arg (=20)
+minimum k value (<=124)
+.TP
+\fB\-\-maxk\fR arg (=60)
+maximum k value (<=124)
+.TP
+\fB\-\-step\fR arg (=10)
+increment of k\-mer of each iteration
+.TP
+\fB\-\-inner_mink\fR arg (=10)
+inner minimum k value
+.TP
+\fB\-\-inner_step\fR arg (=5)
+inner increment of k\-mer
+.TP
+\fB\-\-prefix\fR arg (=3)
+prefix length used to build sub k\-mer table
+.TP
+\fB\-\-min_count\fR arg (=2)
+minimum multiplicity for filtering k\-mer when building the graph
+.TP
+\fB\-\-min_support\fR arg (=1)
+minimum supoort in each iteration
+.TP
+\fB\-\-num_threads\fR arg (=0)
+number of threads
+.TP
+\fB\-\-seed_kmer\fR arg (=30)
+seed kmer size for alignment
+.TP
+\fB\-\-min_contig\fR arg (=200)
+minimum size of contig
+.TP
+\fB\-\-min_transcript\fR arg (=300)
+minimum size of transcript
+.TP
+\fB\-\-similar\fR arg (=0.95)
+similarity for alignment
+.TP
+\fB\-\-max_mismatch\fR arg (=3)
+max mismatch of error correction
+.TP
+\fB\-\-no_local\fR
+do not use local assembly
+.TP
+\fB\-\-no_coverage\fR
+do not iterate on coverage
+.TP
+\fB\-\-no_correct\fR
+do not do correction
+.TP
+\fB\-\-pre_correction\fR
+perform pre\-correction before assembly
+.TP
+\fB\-\-max_isoforms\fR arg (=3)
+maximum number of isoforms
+.TP
+\fB\-\-max_component_size\fR arg (=30)
+maximum size of components
diff --git a/debian/idba_hybrid.1 b/debian/idba_ud.1
similarity index 62%
copy from debian/idba_hybrid.1
copy to debian/idba_ud.1
index 9f0b69e..ca416fe 100644
--- a/debian/idba_hybrid.1
+++ b/debian/idba_ud.1
@@ -1,20 +1,13 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.43.3.
-.TH IDBA_HYBRID "1" "February 2014" "idba_hybrid 1.1.1" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
+.TH IDBA_UD "1" "August 2017" "idba_ud 1.1.3" "User Commands"
 .SH NAME
-idba_hybrid \- Iterative de Bruijn Graph Assembler for hybrid sequencing data
+idba_ud \- Iterative de Bruijn Graph Assembler for hybrid sequencing data
 .SH SYNOPSIS
-.B idba_hybrid
-\fI\-r read.fa \-o output_dir \fR[\fI\-\-reference ref.fa\fR]
+.B idba_ud
+\fI\,-r read.fa -o output_dir\/\fR
 .SH DESCRIPTION
-IDBA-Tran is an iterative De Bruijn Graph De Novo short read assembler
-for transcriptome. It is purely de novo assembler based on only RNA
-sequencing reads. IDBA-Tran uses local assembly to reconstructing
-missing k-mers in low-expressed transcripts and then employs progressive
-cutoff on contigs to separate the graph into components. Each component
-corresponds to one gene in most cases and contains not many transcripts.
-A heuristic algorithm based on pair-end reads is then used to find the
-isoforms.
-.SH OPTIONS
+IDBA\-UD \- Iterative de Bruijn Graph Assembler for sequencing data with 
highly uneven depth.
+.SS "Allowed Options:"
 .TP
 \fB\-o\fR, \fB\-\-out\fR arg (=out)
 output directory
@@ -37,9 +30,6 @@ paired\-end reads fasta for fifth level scaffolds
 \fB\-l\fR, \fB\-\-long_read\fR arg
 fasta long read file (>128)
 .TP
-\fB\-\-reference\fR arg
-reference genome
-.TP
 \fB\-\-mink\fR arg (=20)
 minimum k value (<=124)
 .TP
@@ -73,9 +63,6 @@ seed kmer size for alignment
 \fB\-\-min_contig\fR arg (=200)
 minimum size of contig
 .TP
-\fB\-\-min_region\fR arg (=500)
-minimum size of region in reference genome
-.TP
 \fB\-\-similar\fR arg (=0.95)
 similarity for alignment
 .TP
@@ -85,8 +72,8 @@ max mismatch of error correction
 \fB\-\-min_pairs\fR arg (=3)
 minimum number of pairs
 .TP
-\fB\-\-max_gap\fR arg (=50)
-maximum gap in reference
+\fB\-\-no_bubble\fR
+do not merge bubble
 .TP
 \fB\-\-no_local\fR
 do not use local assembly
diff --git a/debian/links b/debian/links
deleted file mode 100644
index 03be7c0..0000000
--- a/debian/links
+++ /dev/null
@@ -1,2 +0,0 @@
-usr/bin/idba_hybrid                    usr/bin/idba
-usr/share/man/man1/idba_hybrid.1.gz    usr/share/man/man1/idba.1.gz
diff --git a/debian/manpages b/debian/manpages
index 0f65186..0a4f077 100644
--- a/debian/manpages
+++ b/debian/manpages
@@ -1 +1,4 @@
-debian/*.1
+debian/idba.1
+debian/idba_hybrid.1
+debian/idba_tran.1
+debian/idba_ud.1
diff --git a/debian/patches/install_all_idba_flavours.patch 
b/debian/patches/install_all_idba_flavours.patch
new file mode 100644
index 0000000..c61c312
--- /dev/null
+++ b/debian/patches/install_all_idba_flavours.patch
@@ -0,0 +1,28 @@
+Index: idba/bin/Makefile.am
+===================================================================
+--- idba.orig/bin/Makefile.am
++++ idba/bin/Makefile.am
+@@ -36,6 +36,9 @@ split_scaffold_SOURCES = $(top_srcdir)/s
+ sim_reads_SOURCES = $(top_srcdir)/src/release/sim_reads.cpp 
+ 
+ bin_PROGRAMS = \
++      idba \
++      idba_ud \
++      idba_tran \
+       idba_hybrid 
+ 
+ noinst_PROGRAMS = \
+@@ -59,13 +62,10 @@ noinst_PROGRAMS = \
+       split_fq \
+       fq2fa \
+       validate_contigs_blat \
+-      idba_ud \
+       raw_n50 \
+-      idba_tran \
+       parallel_blat \
+       sim_reads_tran \
+       filterfa \
+-      idba \
+       split_scaffold \
+       sim_reads 
+ 
diff --git a/debian/patches/series b/debian/patches/series
index 8a37410..3141c3a 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
+install_all_idba_flavours.patch
 use-atomic-for-mips.patch
 spelling.patch
diff --git a/debian/rules b/debian/rules
index 1b25ad6..12e6cda 100755
--- a/debian/rules
+++ b/debian/rules
@@ -15,5 +15,5 @@ override_dh_auto_configure:
 override_dh_install:
        dh_install
        # for the moment the role of these scripts is totally unknown but they 
do not seem to be necessary
-       rm -f debian/$(DEBPKGNAME)/usr/bin/*.py
-       rm -f debian/$(DEBPKGNAME)/usr/bin/validate_blat*
+       mv debian/$(DEBPKGNAME)/usr/bin/*.py debian/$(DEBPKGNAME)/usr/lib/idba/
+       mv debian/$(DEBPKGNAME)/usr/bin/validate_blat* 
debian/$(DEBPKGNAME)/usr/lib/idba/
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
index d1b9a2c..17ffeb8 100644
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -1,12 +1,34 @@
 Reference:
-  Author: Yu Peng and Henry C. M. Leung and S. M. Yiu and Francis Y. L. Chin
-  Title: "IDBA-UD: a de novo assembler for single-cell and metagenomic 
sequencing data with highly uneven depth"
-  Journal: Bioinformatics
-  Year: 2012
-  Volume: 28
-  Number: 11
-  Pages: 1420-1428
-  DOI: 10.1093/bioinformatics/bts174
-  PMID: 22495754
-  URL: http://bioinformatics.oxfordjournals.org/content/28/11/1420.full
-  eprint: 
http://bioinformatics.oxfordjournals.org/content/28/11/1420.full.pdf+html
+  - Author: Yu Peng and Henry C. M. Leung and S. M. Yiu and Francis Y. L. Chin
+    Title: "IDBA-UD: a de novo assembler for single-cell and metagenomic 
sequencing data with highly uneven depth"
+    Journal: Bioinformatics
+    Year: 2012
+    Volume: 28
+    Number: 11
+    Pages: 1420-1428
+    DOI: 10.1093/bioinformatics/bts174
+    PMID: 22495754
+    URL: http://bioinformatics.oxfordjournals.org/content/28/11/1420.full
+    eprint: 
http://bioinformatics.oxfordjournals.org/content/28/11/1420.full.pdf+html
+  - Author: 
+    Title: IDBA-tran: a more robust de novo de Bruijn graph assembler for 
transcriptomes with uneven expression levels.
+    Journal: Bioinformatics
+    Year: 2013
+    Month: Jul
+    Day: 1
+    Volume: 29
+    Number: 13
+    Pages: i326-i334
+    DOI: 10.1093/bioinformatics/btt219
+    PMID: 23813001 
+    URL: 
https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btt219
+    eprint: 
https://academic.oup.com/bioinformatics/article-pdf/29/13/i326/18534891/btt219.pdf
+Registry:
+  - Name: bio.tools
+    Entry: IDBA
+  - Name: OMICtools
+    Entry: OMICS_01423
+  - Name: OMICtools
+    Entry: OMICS_01318
+  - Name: RRID
+    Entry: SCR_011912

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