[med-svn] [mummer] 05/07: Commit as per 3.23+dfsg-2 upload

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository mummer.

commit 3fd3ad1f69ede037c829d70a51c2f8921e91df08
Author: Andreas Tille <tille at debian.org>
Date:   Sun Feb 4 16:01:44 2018 +0100

    Commit as per 3.23+dfsg-2 upload
---
 .../0009-improve-performance-of-delta2maf.patch    | 56 ----------------------
 debian/patches/series                              |  2 -
 debian/upstream/edam                               | 21 ++++----
 3 files changed, 10 insertions(+), 69 deletions(-)

diff --git a/debian/patches/0009-improve-performance-of-delta2maf.patch b/debian/patches/0009-improve-performance-of-delta2maf.patch
deleted file mode 100644
index 885c402..0000000
--- a/debian/patches/0009-improve-performance-of-delta2maf.patch
+++ /dev/null
@@ -1,56 +0,0 @@
-From: =?utf-8?q?Fabian_Kl=C3=B6tzl?= <fabian at kloetzl.info>
-Date: Fri, 5 Aug 2016 14:14:02 +0200
-Subject: improve performance of delta2maf
-
----
- src/tigr/delta2maf.cc | 23 ++++++++++++++++++++---
- 1 file changed, 20 insertions(+), 3 deletions(-)
-
-diff --git a/src/tigr/delta2maf.cc b/src/tigr/delta2maf.cc
-index f397f35..f47d797 100644
---- a/src/tigr/delta2maf.cc
-+++ b/src/tigr/delta2maf.cc
-@@ -378,8 +378,8 @@ void printAlignments
- 
- {
- 
--  const char * IdR;
--  const char * IdQ;
-+  const char * IdR, *previous_IdR = NULL;
-+  const char * IdQ, *previous_IdQ = NULL;
- 
-   map<string, char *>::iterator finditer;
- 
-@@ -405,6 +405,7 @@ void printAlignments
-   long int sR, eR, sQ, eQ;
-   long int Apos, Bpos;
-   long int SeqLenR, SeqLenQ;
-+  long int previous_SeqLenR = 0, previous_SeqLenQ = 0;
-   int frameR, frameQ;
- 
-   //for ( i = 0; i < LINE_PREFIX_LEN; i ++ )
-@@ -426,7 +427,23 @@ void printAlignments
-       //printf("Looking for R:\"%s\" in map of size %d\n",IdR,seqsMap.size());
-       assert(finditer != seqsMap.end());
-       R = finditer->second;
--      SeqLenR = strlen(R+1);
-+      // SeqLenR = strlen(R+1);
-+
-+      /**
-+       * We don't want to recompute the length of a sequence for each
-+       * iteration. This is especially important as many pairwise alignments
-+       * are split into blocks and we thus do the same thing over and over
-+       * again.
-+       *
-+       * My solution is to simply cache the current length value and reuse
-+       * it in the next iteration given the IDs are equal. This speeds up
-+       * the code by a factor of 20 (in words: twenty).
-+       *
-+       * -- Fabian Klötzl 2016-03-11
-+       */
-+      SeqLenR = IdR == previous_IdR ? previous_SeqLenR : strlen(R + 1);
-+      previous_IdR = IdR;
-+      previous_SeqLenR = SeqLenR;
- 
-       if(DATA_TYPE == NUCMER_DATA){
- 	seqsiter = seqsMapArray.find(make_pair(Ap->idR,1));
diff --git a/debian/patches/series b/debian/patches/series
index 8214868..72bcb76 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -5,6 +5,4 @@ fix_sf_privacy_breach_issue.patch
 hardening.patch
 spelling.patch
 addition_from_mugsy.patch
-addition_from_report_duplicates.patch
-0009-improve-performance-of-delta2maf.patch
 # most probably broken see bug #843621 addition_from_report_duplicates.patch
diff --git a/debian/upstream/edam b/debian/upstream/edam
index 8577214..b7659bc 100644
--- a/debian/upstream/edam
+++ b/debian/upstream/edam
@@ -1,19 +1,18 @@
----
 ontology: EDAM (1.12)
 topic:
   - Sequence analysis
 scopes:
   - name: summary
     function:
-      - Local sequence alignment
-      - Genome alignment
+     - Local sequence alignment
+     - Genome alignment
     inputs:
-      - data: Sequence
-        formats: [FASTA]
+     - data:   Sequence
+       formats: [FASTA]
     outputs:
-      - data: Sequence alignment
-        formats: [Alignment format (text)]
-      - data: Sequence
-        formats: [FASTA]
-      - data: Sequence variations
-        formats: [Textual format]
+     - data:   Sequence alignment
+       formats: [Alignment format (text)]
+     - data:   Sequence
+       formats: [FASTA]
+     - data:   Sequence variations
+       formats: [Textual format]

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/mummer.git