[med-svn] [velvet] 01/01: Add version with MAXKMERLENGTH=127
Andreas Tille
tille at debian.org
Fri Feb 24 09:19:08 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository velvet.
commit a724090fc710d25de29343db0e6df7f7a5c1822d
Author: Andreas Tille <tille at debian.org>
Date: Fri Feb 24 10:11:32 2017 +0100
Add version with MAXKMERLENGTH=127
---
debian/changelog | 6 ++
debian/manpages/velvetg_127.1 | 109 +++++++++++++++++++++++++++++++++++++
debian/manpages/velvetg_127_long.1 | 109 +++++++++++++++++++++++++++++++++++++
debian/manpages/velveth_127.1 | 93 +++++++++++++++++++++++++++++++
debian/manpages/velveth_127_long.1 | 94 ++++++++++++++++++++++++++++++++
debian/rules | 6 ++
debian/velvet-long.install | 2 +
7 files changed, 419 insertions(+)
diff --git a/debian/changelog b/debian/changelog
index cd22543..89c998b 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+velvet (1.2.10+dfsg1-4) experimental; urgency=medium
+
+ * Add version with MAXKMERLENGTH=127
+
+ -- Andreas Tille <tille at debian.org> Fri, 24 Feb 2017 10:10:36 +0100
+
velvet (1.2.10+dfsg1-3) unstable; urgency=medium
* Moved from SVN to Git
diff --git a/debian/manpages/velvetg_127.1 b/debian/manpages/velvetg_127.1
new file mode 100644
index 0000000..dc8fb45
--- /dev/null
+++ b/debian/manpages/velvetg_127.1
@@ -0,0 +1,109 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.45.1.
+.TH VELVETG_127 "1" "July 2014" "velvetg_127 1.2.10+dfsg1" "User Commands"
+.SH NAME
+velvetg_127 \- de Bruijn graph construction, error removal and repeat resolution (MAXKMERLENGTH = 127)
+.SH DESCRIPTION
+Usage:
+\&./velvetg directory [options]
+.TP
+directory
+: working directory name
+.SS "Standard options:"
+.TP
+\fB\-cov_cutoff\fR <floating\-point|auto>
+: removal of low coverage nodes AFTER tour bus or allow the system to infer it
+.IP
+(default: no removal)
+.TP
+\fB\-ins_length\fR <integer>
+: expected distance between two paired end reads (default: no read pairing)
+.TP
+\fB\-read_trkg\fR <yes|no>
+: tracking of short read positions in assembly (default: no tracking)
+.TP
+\fB\-min_contig_lgth\fR <integer>
+: minimum contig length exported to contigs.fa file (default: hash length * 2)
+.TP
+\fB\-amos_file\fR <yes|no>
+: export assembly to AMOS file (default: no export)
+.TP
+\fB\-exp_cov\fR <floating point|auto>
+: expected coverage of unique regions or allow the system to infer it
+.IP
+(default: no long or paired\-end read resolution)
+.HP
+\fB\-long_cov_cutoff\fR <floating\-point>: removal of nodes with low long\-read coverage AFTER tour bus
+.IP
+(default: no removal)
+.SS "Advanced options:"
+.TP
+\fB\-ins_length\fR* <integer>
+: expected distance between two paired\-end reads in the respective short\-read dataset (default: no read pairing)
+.TP
+\fB\-ins_length_long\fR <integer>
+: expected distance between two long paired\-end reads (default: no read pairing)
+.TP
+\fB\-ins_length\fR*_sd <integer>
+: est. standard deviation of respective dataset (default: 10% of corresponding length)
+.IP
+[replace '*' by nothing, '2' or '_long' as necessary]
+.TP
+\fB\-scaffolding\fR <yes|no>
+: scaffolding of contigs used paired end information (default: on)
+.TP
+\fB\-max_branch_length\fR <integer>
+: maximum length in base pair of bubble (default: 100)
+.HP
+\fB\-max_divergence\fR <floating\-point>: maximum divergence rate between two branches in a bubble (default: 0.2)
+.TP
+\fB\-max_gap_count\fR <integer>
+: maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)
+.TP
+\fB\-min_pair_count\fR <integer>
+: minimum number of paired end connections to justify the scaffolding of two long contigs (default: 5)
+.TP
+\fB\-max_coverage\fR <floating point>
+: removal of high coverage nodes AFTER tour bus (default: no removal)
+.TP
+\fB\-coverage_mask\fR <int>
+: minimum coverage required for confident regions of contigs (default: 1)
+.TP
+\fB\-long_mult_cutoff\fR <int>
+: minimum number of long reads required to merge contigs (default: 2)
+.TP
+\fB\-unused_reads\fR <yes|no>
+: export unused reads in UnusedReads.fa file (default: no)
+.TP
+\fB\-alignments\fR <yes|no>
+: export a summary of contig alignment to the reference sequences (default: no)
+.TP
+\fB\-exportFiltered\fR <yes|no>
+: export the long nodes which were eliminated by the coverage filters (default: no)
+.TP
+\fB\-clean\fR <yes|no>
+: remove all the intermediary files which are useless for recalculation (default : no)
+.TP
+\fB\-very_clean\fR <yes|no>
+: remove all the intermediary files (no recalculation possible) (default: no)
+.TP
+\fB\-paired_exp_fraction\fR <double>
+: remove all the paired end connections which less than the specified fraction of the expected count (default: 0.1)
+.TP
+\fB\-shortMatePaired\fR* <yes|no>
+: for mate\-pair libraries, indicate that the library might be contaminated with paired\-end reads (default no)
+.TP
+\fB\-conserveLong\fR <yes|no>
+: preserve sequences with long reads in them (default no)
+.SS "Output:"
+.TP
+directory/contigs.fa
+: fasta file of contigs longer than twice hash length
+.TP
+directory/stats.txt
+: stats file (tab\-spaced) useful for determining appropriate coverage cutoff
+.TP
+directory/LastGraph
+: special formatted file with all the information on the final graph
+.TP
+directory/velvet_asm.afg
+: (if requested) AMOS compatible assembly file
diff --git a/debian/manpages/velvetg_127_long.1 b/debian/manpages/velvetg_127_long.1
new file mode 100644
index 0000000..b0b0a68
--- /dev/null
+++ b/debian/manpages/velvetg_127_long.1
@@ -0,0 +1,109 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.45.1.
+.TH VELVETG_127_LONG "1" "July 2014" "velvetg_127_long 1.2.10+dfsg1" "User Commands"
+.SH NAME
+velvetg_127_long \- de Bruijn graph construction, error removal and repeat resolution (MAXKMERLENGTH = 127, LONGSEQUENCES)
+.SH DESCRIPTION
+Usage:
+\&./velvetg directory [options]
+.TP
+directory
+: working directory name
+.SS "Standard options:"
+.TP
+\fB\-cov_cutoff\fR <floating\-point|auto>
+: removal of low coverage nodes AFTER tour bus or allow the system to infer it
+.IP
+(default: no removal)
+.TP
+\fB\-ins_length\fR <integer>
+: expected distance between two paired end reads (default: no read pairing)
+.TP
+\fB\-read_trkg\fR <yes|no>
+: tracking of short read positions in assembly (default: no tracking)
+.TP
+\fB\-min_contig_lgth\fR <integer>
+: minimum contig length exported to contigs.fa file (default: hash length * 2)
+.TP
+\fB\-amos_file\fR <yes|no>
+: export assembly to AMOS file (default: no export)
+.TP
+\fB\-exp_cov\fR <floating point|auto>
+: expected coverage of unique regions or allow the system to infer it
+.IP
+(default: no long or paired\-end read resolution)
+.HP
+\fB\-long_cov_cutoff\fR <floating\-point>: removal of nodes with low long\-read coverage AFTER tour bus
+.IP
+(default: no removal)
+.SS "Advanced options:"
+.TP
+\fB\-ins_length\fR* <integer>
+: expected distance between two paired\-end reads in the respective short\-read dataset (default: no read pairing)
+.TP
+\fB\-ins_length_long\fR <integer>
+: expected distance between two long paired\-end reads (default: no read pairing)
+.TP
+\fB\-ins_length\fR*_sd <integer>
+: est. standard deviation of respective dataset (default: 10% of corresponding length)
+.IP
+[replace '*' by nothing, '2' or '_long' as necessary]
+.TP
+\fB\-scaffolding\fR <yes|no>
+: scaffolding of contigs used paired end information (default: on)
+.TP
+\fB\-max_branch_length\fR <integer>
+: maximum length in base pair of bubble (default: 100)
+.HP
+\fB\-max_divergence\fR <floating\-point>: maximum divergence rate between two branches in a bubble (default: 0.2)
+.TP
+\fB\-max_gap_count\fR <integer>
+: maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)
+.TP
+\fB\-min_pair_count\fR <integer>
+: minimum number of paired end connections to justify the scaffolding of two long contigs (default: 5)
+.TP
+\fB\-max_coverage\fR <floating point>
+: removal of high coverage nodes AFTER tour bus (default: no removal)
+.TP
+\fB\-coverage_mask\fR <int>
+: minimum coverage required for confident regions of contigs (default: 1)
+.TP
+\fB\-long_mult_cutoff\fR <int>
+: minimum number of long reads required to merge contigs (default: 2)
+.TP
+\fB\-unused_reads\fR <yes|no>
+: export unused reads in UnusedReads.fa file (default: no)
+.TP
+\fB\-alignments\fR <yes|no>
+: export a summary of contig alignment to the reference sequences (default: no)
+.TP
+\fB\-exportFiltered\fR <yes|no>
+: export the long nodes which were eliminated by the coverage filters (default: no)
+.TP
+\fB\-clean\fR <yes|no>
+: remove all the intermediary files which are useless for recalculation (default : no)
+.TP
+\fB\-very_clean\fR <yes|no>
+: remove all the intermediary files (no recalculation possible) (default: no)
+.TP
+\fB\-paired_exp_fraction\fR <double>
+: remove all the paired end connections which less than the specified fraction of the expected count (default: 0.1)
+.TP
+\fB\-shortMatePaired\fR* <yes|no>
+: for mate\-pair libraries, indicate that the library might be contaminated with paired\-end reads (default no)
+.TP
+\fB\-conserveLong\fR <yes|no>
+: preserve sequences with long reads in them (default no)
+.SS "Output:"
+.TP
+directory/contigs.fa
+: fasta file of contigs longer than twice hash length
+.TP
+directory/stats.txt
+: stats file (tab\-spaced) useful for determining appropriate coverage cutoff
+.TP
+directory/LastGraph
+: special formatted file with all the information on the final graph
+.TP
+directory/velvet_asm.afg
+: (if requested) AMOS compatible assembly file
diff --git a/debian/manpages/velveth_127.1 b/debian/manpages/velveth_127.1
new file mode 100644
index 0000000..98eaa28
--- /dev/null
+++ b/debian/manpages/velveth_127.1
@@ -0,0 +1,93 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.45.1.
+.TH VELVETH_127 "1" "July 2014" "velveth_127 1.2.10+dfsg1" "User Commands"
+.SH NAME
+velveth_127 \- simple hashing program (MAXKMERLENGTH = 127)
+.SH DESCRIPTION
+velveth \- simple hashing program
+Version 1.2.09
+.SH OPTIONS
+.TP
+\fB\-strand_specific\fR
+: for strand specific transcriptome sequencing data (default: off)
+.TP
+\fB\-reuse_Sequences\fR
+: reuse Sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
+.TP
+\fB\-reuse_binary\fR
+: reuse binary sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
+.TP
+\fB\-noHash\fR
+: simply prepare Sequences file, do not hash reads or prepare Roadmaps file (default: off)
+.TP
+\fB\-create_binary\fR
+: create binary CnyUnifiedSeq file (default: off)
+.PP
+Synopsis:
+.SS "- Short single end reads:"
+.IP
+velveth Assem 29 \fB\-short\fR \fB\-fastq\fR s_1_sequence.txt
+.SS "- Paired-end short reads (remember to interleave paired reads):"
+.IP
+velveth Assem 31 \fB\-shortPaired\fR \fB\-fasta\fR interleaved.fna
+.PP
+\- Paired\-end short reads (using separate files for the paired reads)
+.IP
+velveth Assem 31 \fB\-shortPaired\fR \fB\-fasta\fR \fB\-separate\fR left.fa right.fa
+.SS "- Two channels and some long reads:"
+.IP
+velveth Assem 43 \fB\-short\fR \fB\-fastq\fR unmapped.fna \fB\-longPaired\fR \fB\-fasta\fR SangerReads.fasta
+.SS "- Three channels:"
+.IP
+velveth Assem 35 \fB\-shortPaired\fR \fB\-fasta\fR pe_lib1.fasta \fB\-shortPaired2\fR pe_lib2.fasta \fB\-short3\fR se_lib1.fa
+.SS "Output:"
+.IP
+directory/Roadmaps
+directory/Sequences
+.IP
+[Both files are picked up by graph, so please leave them there]
+.SH COPYRIGHT
+Copyright 2007, 2008 Daniel Zerbino (zerbino at ebi.ac.uk)
+.br
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+.PP
+Compilation settings:
+CATEGORIES = 2
+MAXKMERLENGTH = 127
+OPENMP
+.PP
+Usage:
+\&./velveth directory hash_length {[\-file_format][\-read_type][\-separate|\-interleaved] filename1 [filename2 ...]} {...} [options]
+.TP
+directory
+: directory name for output files
+.TP
+hash_length
+: EITHER an odd integer (if even, it will be decremented) <= 127 (if above, will be reduced)
+: OR: m,M,s where m and M are odd integers (if not, they will be decremented) with m < M <= 127 (if above, will be reduced)
+.IP
+and s is a step (even number). Velvet will then hash from k=m to k=M with a step of s
+.TP
+filename
+: path to sequence file or \- for standard input
+.SS "File format options:"
+.HP
+\fB\-fasta\fR \fB\-fastq\fR \fB\-raw\fR \fB\-fasta\fR.gz \fB\-fastq\fR.gz \fB\-raw\fR.gz \fB\-sam\fR \fB\-bam\fR \fB\-fmtAuto\fR
+.IP
+(Note: \fB\-fmtAuto\fR will detect fasta or fastq, and will try the following programs for decompression : gunzip, pbunzip2, bunzip2
+.SS "File layout options for paired reads (only for fasta and fastq formats):"
+.TP
+\fB\-interleaved\fR
+: File contains paired reads interleaved in the one file (default)
+.TP
+\fB\-separate\fR
+: Read 2 separate files for paired reads
+.SS "Read type options:"
+.HP
+\fB\-short\fR \fB\-shortPaired\fR
+.HP
+\fB\-short2\fR \fB\-shortPaired2\fR
+.HP
+\fB\-long\fR \fB\-longPaired\fR
+.HP
+\fB\-reference\fR
diff --git a/debian/manpages/velveth_127_long.1 b/debian/manpages/velveth_127_long.1
new file mode 100644
index 0000000..38ac9cd
--- /dev/null
+++ b/debian/manpages/velveth_127_long.1
@@ -0,0 +1,94 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.45.1.
+.TH VELVETH_127_LONG "1" "July 2014" "velveth_127_long 1.2.10+dfsg1" "User Commands"
+.SH NAME
+velveth_127_long \- simple hashing program (MAXKMERLENGTH = 127, LONGSEQUENCES)
+.SH DESCRIPTION
+velveth \- simple hashing program
+Version 1.2.09
+.SH OPTIONS
+.TP
+\fB\-strand_specific\fR
+: for strand specific transcriptome sequencing data (default: off)
+.TP
+\fB\-reuse_Sequences\fR
+: reuse Sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
+.TP
+\fB\-reuse_binary\fR
+: reuse binary sequences file (or link) already in directory (no need to provide original filenames in this case (default: off)
+.TP
+\fB\-noHash\fR
+: simply prepare Sequences file, do not hash reads or prepare Roadmaps file (default: off)
+.TP
+\fB\-create_binary\fR
+: create binary CnyUnifiedSeq file (default: off)
+.PP
+Synopsis:
+.SS "- Short single end reads:"
+.IP
+velveth Assem 29 \fB\-short\fR \fB\-fastq\fR s_1_sequence.txt
+.SS "- Paired-end short reads (remember to interleave paired reads):"
+.IP
+velveth Assem 31 \fB\-shortPaired\fR \fB\-fasta\fR interleaved.fna
+.PP
+\- Paired\-end short reads (using separate files for the paired reads)
+.IP
+velveth Assem 31 \fB\-shortPaired\fR \fB\-fasta\fR \fB\-separate\fR left.fa right.fa
+.SS "- Two channels and some long reads:"
+.IP
+velveth Assem 43 \fB\-short\fR \fB\-fastq\fR unmapped.fna \fB\-longPaired\fR \fB\-fasta\fR SangerReads.fasta
+.SS "- Three channels:"
+.IP
+velveth Assem 35 \fB\-shortPaired\fR \fB\-fasta\fR pe_lib1.fasta \fB\-shortPaired2\fR pe_lib2.fasta \fB\-short3\fR se_lib1.fa
+.SS "Output:"
+.IP
+directory/Roadmaps
+directory/Sequences
+.IP
+[Both files are picked up by graph, so please leave them there]
+.SH COPYRIGHT
+Copyright 2007, 2008 Daniel Zerbino (zerbino at ebi.ac.uk)
+.br
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+.PP
+Compilation settings:
+CATEGORIES = 2
+MAXKMERLENGTH = 127
+OPENMP
+LONGSEQUENCES
+.PP
+Usage:
+\&./velveth directory hash_length {[\-file_format][\-read_type][\-separate|\-interleaved] filename1 [filename2 ...]} {...} [options]
+.TP
+directory
+: directory name for output files
+.TP
+hash_length
+: EITHER an odd integer (if even, it will be decremented) <= 127 (if above, will be reduced)
+: OR: m,M,s where m and M are odd integers (if not, they will be decremented) with m < M <= 127 (if above, will be reduced)
+.IP
+and s is a step (even number). Velvet will then hash from k=m to k=M with a step of s
+.TP
+filename
+: path to sequence file or \- for standard input
+.SS "File format options:"
+.HP
+\fB\-fasta\fR \fB\-fastq\fR \fB\-raw\fR \fB\-fasta\fR.gz \fB\-fastq\fR.gz \fB\-raw\fR.gz \fB\-sam\fR \fB\-bam\fR \fB\-fmtAuto\fR
+.IP
+(Note: \fB\-fmtAuto\fR will detect fasta or fastq, and will try the following programs for decompression : gunzip, pbunzip2, bunzip2
+.SS "File layout options for paired reads (only for fasta and fastq formats):"
+.TP
+\fB\-interleaved\fR
+: File contains paired reads interleaved in the one file (default)
+.TP
+\fB\-separate\fR
+: Read 2 separate files for paired reads
+.SS "Read type options:"
+.HP
+\fB\-short\fR \fB\-shortPaired\fR
+.HP
+\fB\-short2\fR \fB\-shortPaired2\fR
+.HP
+\fB\-long\fR \fB\-longPaired\fR
+.HP
+\fB\-reference\fR
diff --git a/debian/rules b/debian/rules
index 2606112..e4b4dfc 100755
--- a/debian/rules
+++ b/debian/rules
@@ -30,6 +30,12 @@ build_long_versions :
#And also one with both options
dh_auto_build -- MAXKMERLENGTH=63 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)"
mv velveth velveth_63_long ; mv velvetg velvetg_63_long
+ #Make _127 kmer version
+ dh_auto_build -- MAXKMERLENGTH=127 velveth velvetg OPENMP=1 CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)"
+ mv velveth velveth_127 ; mv velvetg velvetg_127
+ #And also one with both options
+ dh_auto_build -- MAXKMERLENGTH=127 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)"
+ mv velveth velveth_127_long ; mv velvetg velvetg_127_long
override_dh_auto_build : build_long_versions
touch zlib # prevents the zlib in the ‘third-party’ folder to be built.
diff --git a/debian/velvet-long.install b/debian/velvet-long.install
index c61f09d..92f8977 100644
--- a/debian/velvet-long.install
+++ b/debian/velvet-long.install
@@ -1,3 +1,5 @@
velvet?_63 usr/bin
velvet?_long usr/bin
velvet?_63_long usr/bin
+velvet?_127 usr/bin
+velvet?_127_long usr/bin
--
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