[med-svn] [sprai] 01/03: Imported Upstream version 0.9.9.21+dfsg

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository sprai.

commit 45cd8a23be3e20d12661a56c006dcf330c6d3389
Author: Afif Elghraoui <afif at debian.org>
Date:   Mon Nov 7 21:01:25 2016 -0800

    Imported Upstream version 0.9.9.21+dfsg
---
 check_circularity.pl                  | 1 +
 doc/_build/html/_sources/Download.txt | 6 +++++-
 doc/_build/html/_sources/index.txt    | 4 ++++
 ezez4makefile_v4.pl                   | 2 +-
 makefile                              | 2 +-
 wscript                               | 2 +-
 6 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/check_circularity.pl b/check_circularity.pl
index 5f98c96..7f819cb 100755
--- a/check_circularity.pl
+++ b/check_circularity.pl
@@ -121,6 +121,7 @@ for my $seq_obj (@sequence_objects) {
     # Fields: query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
     my ($query_id, $subj_id, $ident_percent, $align_len, $mismatches, $gap_opens, $qstart, $qend, $sstart, $send, $evalue, $bit_score) = split(/\t/);
     next if($qstart == $sstart && $qend == $send);
+    next if($sstart >=$send);
     next if($align_len < $param_min_overlap_len);
     next if($ident_percent < $param_alert_overlap_match_ratio * 100.0);
     print STDERR "  len=$seq_obj->{len} [$qstart-$qend] => [$sstart-$send]\n" if($debug);
diff --git a/doc/_build/html/_sources/Download.txt b/doc/_build/html/_sources/Download.txt
index f104a7c..e8973e4 100644
--- a/doc/_build/html/_sources/Download.txt
+++ b/doc/_build/html/_sources/Download.txt
@@ -1,11 +1,15 @@
 ===========================
 Download The Latest Version
 ===========================
-http://zombie.cb.k.u-tokyo.ac.jp/sprai/dist/sprai-0.9.9.18.tar.gz
+http://zombie.cb.k.u-tokyo.ac.jp/sprai/dist/sprai-0.9.9.20.tar.gz
 
 ==============
 Older releases
 ==============
+http://zombie.cb.k.u-tokyo.ac.jp/sprai/dist/sprai-0.9.9.19.tar.gz
+
+http://zombie.cb.k.u-tokyo.ac.jp/sprai/dist/sprai-0.9.9.18.tar.gz
+
 http://zombie.cb.k.u-tokyo.ac.jp/sprai/dist/sprai-0.9.9.17.tar.gz
 
 http://zombie.cb.k.u-tokyo.ac.jp/sprai/dist/sprai-0.9.9.16.tar.gz
diff --git a/doc/_build/html/_sources/index.txt b/doc/_build/html/_sources/index.txt
index d855879..720e258 100644
--- a/doc/_build/html/_sources/index.txt
+++ b/doc/_build/html/_sources/index.txt
@@ -20,6 +20,10 @@ Contents
 
 Changelogs
 =============
+2016.10.19 v0.9.9.20 ezez4makefile_v4.pl: an error message was modified. (Thanks to Yuuki Kobayashi for a report and Tomoaki Nishiyama for code modification)
+
+2016.8.5 v0.9.9.19: ezez_vx1.pl: use the blast_path parameter. (Thanks to Rajanikanth Govindarajulu for a report)
+
 2016.6.19 v0.9.9.18: myrealgner.c: initial colsize was changed. (Thanks to Takahiro Bino for a report)
 
 2016.6.3 v0.9.9.17: use_one_subread option in ec.spec: if not 0, use one subread per one molecule. (Thanks to Tomoaki Nishiyama for advice)
diff --git a/ezez4makefile_v4.pl b/ezez4makefile_v4.pl
index 8fb62cf..0b41df1 100755
--- a/ezez4makefile_v4.pl
+++ b/ezez4makefile_v4.pl
@@ -110,7 +110,7 @@ if(defined($params{input_for_database})){
   printf STDERR "number of libraries: $nlibs\n";
   printf STDERR "libs: @input_libs\n";
 }else{
-  die "specify input_fastq in ec.spec\n";
+  die "specify input_for_database in ec.spec\n";
 }
 
 if(defined($params{estimated_genome_size})){
diff --git a/makefile b/makefile
index 233c53a..8ff6771 100644
--- a/makefile
+++ b/makefile
@@ -1,5 +1,5 @@
 APPNAME = 'sprai'
-VERSION = '0.9.9.19'
+VERSION = '0.9.9.21'
 
 PREFIX=$(PWD)
 COMPILED= \
diff --git a/wscript b/wscript
index 53f8cec..604a5f8 100644
--- a/wscript
+++ b/wscript
@@ -1,5 +1,5 @@
 APPNAME = 'sprai'
-VERSION = '0.9.9.19'
+VERSION = '0.9.9.21'
 
 srcdir = '.'
 blddir = 'build'

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