This is an automated email from the git hooks/post-receive script. afif pushed a commit to branch master in repository sprai.
commit c078e5ff21dcd06193c8fc9d4267f53a86aea6cd Author: Afif Elghraoui <[email protected]> Date: Tue Jun 7 19:09:05 2016 -0700 Imported Upstream version 0.9.9.17+dfsg --- doc/_build/html/_sources/Download.txt | 4 +++- doc/_build/html/_sources/index.txt | 4 +++- ec.spec | 3 +++ ezez4makefile_v4.pl | 8 ++++++++ ezez4qsub_vx1.pl | 9 +++++++++ ezez_vx1.pl | 8 ++++++++ makefile | 2 +- wscript | 2 +- 8 files changed, 36 insertions(+), 4 deletions(-) diff --git a/doc/_build/html/_sources/Download.txt b/doc/_build/html/_sources/Download.txt index b658f02..4c0f946 100644 --- a/doc/_build/html/_sources/Download.txt +++ b/doc/_build/html/_sources/Download.txt @@ -1,11 +1,13 @@ =========================== Download The Latest Version =========================== -http://zombie.cb.k.u-tokyo.ac.jp/sprai/dist/sprai-0.9.9.15.tar.gz +http://zombie.cb.k.u-tokyo.ac.jp/sprai/dist/sprai-0.9.9.16.tar.gz ============== Older releases ============== +http://zombie.cb.k.u-tokyo.ac.jp/sprai/dist/sprai-0.9.9.15.tar.gz + http://zombie.cb.k.u-tokyo.ac.jp/sprai/dist/sprai-0.9.9.14.tar.gz http://zombie.cb.k.u-tokyo.ac.jp/sprai/dist/sprai-0.9.9.13.tar.gz diff --git a/doc/_build/html/_sources/index.txt b/doc/_build/html/_sources/index.txt index 317a77a..ece3817 100644 --- a/doc/_build/html/_sources/index.txt +++ b/doc/_build/html/_sources/index.txt @@ -20,7 +20,9 @@ Contents Changelogs ============= -2016.5.31 v0.9.9.15: ezez4makefile_v4.pl was added. You can use Makefile when execute Sprai. (Thanks to Tomoaki Nishiyama for code modifications) +2016.6.1 v0.9.9.16: ezez_vx1.pl & ezez4qsub_vx1.pl: set -o pipefail was added. + +2016.5.31 v0.9.9.15: ezez4makefile_v4.pl was added. You can use Makefile when execute Sprai. See README. (Thanks to Tomoaki Nishiyama for code modifications) 2016.4.15: v0.9.9.14: -ec_only mode can be run without a spec file of Celera Assembler. (Thanks to Afif Elghraoui for a report) diff --git a/ec.spec b/ec.spec index df49b5d..1c16fd3 100644 --- a/ec.spec +++ b/ec.spec @@ -52,6 +52,9 @@ max_target_seqs 100 #trim: both ends of each alignment by blastn will be trimmed 'trim' bases to detect chimeric reads trim 42 +# if not 0, use only one subread per one molecule +use_one_subread 0 + # direct_vote & copy_blastdb are used by ezez4makefile_v4.pl direct_vote 0 # skip writing the blast results once to disk before selecting diff --git a/ezez4makefile_v4.pl b/ezez4makefile_v4.pl index bc83b9c..8fb62cf 100755 --- a/ezez4makefile_v4.pl +++ b/ezez4makefile_v4.pl @@ -95,6 +95,7 @@ my $param_assembly_rreq = ""; my $filter_same_lib = "| cat"; my $min_len_for_query=1; my $max_len_for_query=1000000000000000; +my $use_one_subread=0; my $command=""; @@ -182,6 +183,9 @@ if(defined($params{max_read_length})){ if(defined($params{trim})){ $trim = $params{trim}; } +if(defined($params{use_one_subread})){ + $use_one_subread = $params{use_one_subread}; +} if(defined($params{ca_path})){ $ca_path = $params{ca_path}; } @@ -264,6 +268,7 @@ if($max_target_seqs){ } printf STDERR ("valid_voters %s\n",join(" ", @voters)); printf STDERR ("trim %d\n",$trim); +printf STDERR ("use_one_subread %d\n",$use_one_subread); printf STDERR ("ca_path %s\n",$ca_path); printf STDERR ("blast_path %s\n",$blast_path); printf STDERR ("sprai_path %s\n",$sprai_path); @@ -362,6 +367,9 @@ for($libi = 0; $libi < $nlibs; $libi++){ my $PG0="$bindir/fa2fq.pl"; my $PG2="$bindir/fqfilt.pl"; my $PG3="$bindir/dumbbell_filter.pl"; + if(!$use_one_subread){ + $PG3="cat"; + } my $command = "STMP=`mktemp -d --tmpdir sprai-XXXXXX` ; set -o pipefail; $PG0 \$\< | $PG3 - | $PG - --prefix $iprefix | gzip -c -1 > \$\$STMP/c_l${libi}.idfq.gz && cp -p \$\$STMP/c_l${libi}.idfq.gz \$@ && openssl dgst \$\$STMP/c_l${libi}.idfq.gz \$@; status=\$\$?; rm -fr \$\$STMP;exit \$\$status"; $rreq = ""; diff --git a/ezez4qsub_vx1.pl b/ezez4qsub_vx1.pl index 6ed1751..67db42d 100755 --- a/ezez4qsub_vx1.pl +++ b/ezez4qsub_vx1.pl @@ -130,6 +130,7 @@ my $min_len_for_query=1; my $max_len_for_query=1000000000000000; my $sge=""; my $estimated_depth=0; +my $use_one_subread=0; if(defined($params{input_for_database})){ $input_for_database = $params{input_for_database}; @@ -235,6 +236,10 @@ if(defined($params{max_target_seqs})){ $max_target_seqs = $params{max_target_seqs}; } +if(defined($params{use_one_subread})){ + $use_one_subread = $params{use_one_subread}; +} + printf STDERR ("#>- params -<#\n"); printf STDERR ("input_for_database %s\n",$input_for_database); printf STDERR ("estimated_genome_size %g\n",$estimated_genome_size); @@ -250,6 +255,7 @@ printf STDERR ("evalue %g\n",$evalue); printf STDERR ("num_threads %d\n",$num_threads); printf STDERR ("valid_voters %s\n",$valid_voters); printf STDERR ("trim %d\n",$trim); +printf STDERR ("use_one_subread %d\n",$use_one_subread); if($ca_path){ printf STDERR ("ca_path %s\n",$ca_path); } @@ -371,6 +377,9 @@ if($from == 0) my $PG = "$bindir/fq2idfq.pl"; my $PG2 = "$bindir/fqfilt.pl"; my $dumbbell_filter = "$bindir/dumbbell_filter.pl"; + if(!$use_one_subread){ + $dumbbell_filter = "cat"; + } if($input_for_database !~ /^\//){ $input_for_database = sprintf("$pwd/$input_for_database"); diff --git a/ezez_vx1.pl b/ezez_vx1.pl index f470750..a4abbd3 100755 --- a/ezez_vx1.pl +++ b/ezez_vx1.pl @@ -94,6 +94,7 @@ my $word_size=0; my $min_len_for_query=1; my $max_len_for_query=1000000000000000; my $estimated_depth=0; +my $use_one_subread=0; my $blasr_path=""; my $blasr_opt=""; @@ -184,6 +185,9 @@ if(defined($params{max_len_for_query})){ if(defined($params{max_target_seqs})){ $max_target_seqs = $params{max_target_seqs}; } +if(defined($params{use_one_subread})){ + $use_one_subread = $params{use_one_subread}; +} printf STDERR ("#>- params -<#\n"); printf STDERR ("input_for_database %s\n",$input_for_database); @@ -196,6 +200,7 @@ printf STDERR ("evalue %g\n",$evalue); printf STDERR ("num_threads %d\n",$num_threads); printf STDERR ("valid_voters %s\n",$valid_voters); printf STDERR ("trim %d\n",$trim); +printf STDERR ("use_one_subread %d\n",$use_one_subread); if($ca_path){ printf STDERR ("ca_path %s\n",$ca_path); } @@ -287,6 +292,9 @@ if($from == 0) if($sprai_path){ $dumbbell_filter = "$sprai_path/$dumbbell_filter"; } + if(!$use_one_subread){ + $dumbbell_filter = "cat"; + } my $com1; my $com2; diff --git a/makefile b/makefile index 8f78f13..efeae27 100644 --- a/makefile +++ b/makefile @@ -1,5 +1,5 @@ APPNAME = 'sprai' -VERSION = '0.9.9.16' +VERSION = '0.9.9.17' PREFIX=$(PWD) COMPILED= \ diff --git a/wscript b/wscript index 645b700..7ca444a 100644 --- a/wscript +++ b/wscript @@ -1,5 +1,5 @@ APPNAME = 'sprai' -VERSION = '0.9.9.16' +VERSION = '0.9.9.17' srcdir = '.' blddir = 'build' -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sprai.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
