[med-svn] [iva] 03/03: new upstream version

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository iva.

commit bbe0a2e5251b4e55216ca7a53a94fcc542d8e8c3
Author: Sascha Steinbiss <satta at debian.org>
Date:   Tue Sep 6 12:22:41 2016 +0000

    new upstream version
---
 debian/changelog              |  9 +++++++++
 debian/control                |  2 +-
 debian/iva.lintian-overrides  |  2 --
 debian/patches/series         |  2 +-
 debian/patches/spelling.patch | 27 +++++++++++----------------
 5 files changed, 22 insertions(+), 20 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index ba446e1..f21cb38 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,12 @@
+iva (1.0.7+ds-1) unstable; urgency=medium
+
+  * Add Vcs-Git.
+  * Update uploader email.
+  * New upstream release.
+  * Drop patches applied by upstream.
+
+ -- Sascha Steinbiss <satta at debian.org>  Tue, 06 Sep 2016 10:59:10 +0000
+
 iva (1.0.6+ds-1) unstable; urgency=medium
 
   * New upstream release.
diff --git a/debian/control b/debian/control
index cd8fc3a..8520970 100644
--- a/debian/control
+++ b/debian/control
@@ -2,7 +2,7 @@ Source: iva
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille at debian.org>,
            Jorge Soares <j.s.soares at gmail.com>,
-           Sascha Steinbiss <sascha at steinbiss.name>
+           Sascha Steinbiss <satta at debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 9),
diff --git a/debian/iva.lintian-overrides b/debian/iva.lintian-overrides
deleted file mode 100644
index 354f2f4..0000000
--- a/debian/iva.lintian-overrides
+++ /dev/null
@@ -1,2 +0,0 @@
-# this file is not generated but provided by upstream
-iva: package-contains-timestamped-gzip
diff --git a/debian/patches/series b/debian/patches/series
index f1dc111..ccc43b9 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,2 @@
+spelling.patch
 add-shebang-line-to-getMummerStats
-adjust_required_pysam_version.patch
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
index 463be8a..128dec1 100644
--- a/debian/patches/spelling.patch
+++ b/debian/patches/spelling.patch
@@ -1,18 +1,13 @@
 Description: spelling fixes
-Author: Sascha Steinbiss <sascha at steinbiss.name>
---- a/scripts/iva
-+++ b/scripts/iva
-@@ -15,10 +15,10 @@
+Author: Sascha Steinbiss <satta at debian.org>
+--- a/scripts/iva_qc_make_db
++++ b/scripts/iva_qc_make_db
+@@ -23,7 +23,7 @@
+ )
  
- 
- io_group = parser.add_argument_group('Input and output')
--io_group.add_argument('-f', '--reads_fwd', action=iva.common.abspathAction, help='Name of forward reads fasta/q file. Must be used in conjuction with --reads_rev', metavar='filename[.gz]')
--io_group.add_argument('-r', '--reads_rev', action=iva.common.abspathAction, help='Name of reverse reads fasta/q file. Must be used in conjuction with --reads_fwd', metavar='filename[.gz]')
-+io_group.add_argument('-f', '--reads_fwd', action=iva.common.abspathAction, help='Name of forward reads fasta/q file. Must be used in conjunction with --reads_rev', metavar='filename[.gz]')
-+io_group.add_argument('-r', '--reads_rev', action=iva.common.abspathAction, help='Name of reverse reads fasta/q file. Must be used in conjunction with --reads_fwd', metavar='filename[.gz]')
- io_group.add_argument('--fr', action=iva.common.abspathAction, dest='reads', help='Name of interleaved fasta/q file', metavar='filename[.gz]')
--io_group.add_argument('--keep_files', action='store_true', help='Keep intermediate files (could be many!). Default is to delete all unecessary files')
-+io_group.add_argument('--keep_files', action='store_true', help='Keep intermediate files (could be many!). Default is to delete all unnecessary files')
- io_group.add_argument('--contigs', action=iva.common.abspathAction, help='Fasta file of contigs to be extended. Incompatible with --reference', metavar='filename[.gz]')
- io_group.add_argument('--reference', action=iva.common.abspathAction, help='Fasta file of reference genome, or parts thereof. IVA will try to assemble one contig per sequence in this file. Incompatible with --contigs', metavar='filename[.gz]')
- io_group.add_argument('-v', '--verbose', action='count', help='Be verbose by printing messages to stdout. Use up to three times for increasing verbosity.', default=0)
+ parser.add_argument('outdir', help='Name of output directory', metavar='Directory_name')
+-parser.add_argument('--add_to_ref', action=iva.common.abspathAction, help='Filename of Genbank IDs or GI numbers to be added to database. Format is: whitespace separated list of GI numbers on each line. One line defines one genome (e.g. flu is 8 segements, so put 8 GI numbers on one line for one flu reference)', metavar='Filename')
++parser.add_argument('--add_to_ref', action=iva.common.abspathAction, help='Filename of Genbank IDs or GI numbers to be added to database. Format is: whitespace separated list of GI numbers on each line. One line defines one genome (e.g. flu is 8 segments, so put 8 GI numbers on one line for one flu reference)', metavar='Filename')
+ parser.add_argument('--skip_viruses', action='store_true', help='Do not run kraken-build --download-library viruses when building the database. If this option used, then --add_to_ref must also be used')
+ parser.add_argument('--threads', type=int, help='Number of threads to use [%(default)s]', metavar='INT', default=1)
+ parser.add_argument('--minimizer_len', type=int, help='Number to pass to kraken-build minimizer_len option [%(default)s]', default=13, metavar='INT')

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