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commit 3fd3ad1f69ede037c829d70a51c2f8921e91df08
Author: Andreas Tille <ti...@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?= <fab...@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]
--
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