[med-svn] [Git][med-team/kraken2][master] 5 commits: routine-update: New upstream version
Nilesh Patra
gitlab at salsa.debian.org
Thu Nov 12 17:59:21 GMT 2020
Nilesh Patra pushed to branch master at Debian Med / kraken2
Commits:
4c6325f4 by Nilesh Patra at 2020-11-12T23:23:45+05:30
routine-update: New upstream version
- - - - -
48fd9876 by Nilesh Patra at 2020-11-12T23:23:46+05:30
New upstream version 2.1.1
- - - - -
91ac2ce6 by Nilesh Patra at 2020-11-12T23:23:48+05:30
Update upstream source from tag 'upstream/2.1.1'
Update to upstream version '2.1.1'
with Debian dir 2dd548dd03bf0e217771a1ec05a2e3655fba8ab5
- - - - -
cbad7953 by Nilesh Patra at 2020-11-12T23:25:48+05:30
Remove patch implemented upstream
- - - - -
c019d905 by Nilesh Patra at 2020-11-12T23:26:29+05:30
routine-update: Ready to upload to unstable
- - - - -
9 changed files:
- CHANGELOG.md
- debian/changelog
- − debian/patches/include_kraken2_headers.patch
- debian/patches/series
- docs/MANUAL.html
- docs/top.html
- install_kraken2.sh
- scripts/standard_installation.sh
- src/hyperloglogplus.h
Changes:
=====================================
CHANGELOG.md
=====================================
@@ -1,5 +1,12 @@
# Changelog
+## [2.1.1] - 2020-11-08
+
+### Fixed
+- Compilation error with GCC 10, omission of cstdint header
+- Removed --skip-maps from standard install due to addition of plasmids,
+ which require acc/taxid maps
+
## [2.1.0] - 2020-10-13
### Added
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+kraken2 (2.1.1-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+
+ -- Nilesh Patra <npatra974 at gmail.com> Thu, 12 Nov 2020 23:26:29 +0530
+
kraken2 (2.1.0-1) unstable; urgency=medium
* New upstream version
=====================================
debian/patches/include_kraken2_headers.patch deleted
=====================================
@@ -1,14 +0,0 @@
-Author: Nilesh Patra <npatra974 at gmail.com>
-Description: Include kraken2 headers in hyperloglogplus.h
-Last-Changed: October 14, 2020
-Forwarded: https://github.com/DerrickWood/kraken2/pull/340
---- a/src/hyperloglogplus.h
-+++ b/src/hyperloglogplus.h
-@@ -13,6 +13,7 @@
- #ifndef HYPERLOGLOGPLUS_H_
- #define HYPERLOGLOGPLUS_H_
-
-+#include "kraken2_headers.h"
- #include<vector>
- #include<unordered_set>
- using namespace std;
=====================================
debian/patches/series
=====================================
@@ -1,4 +1,3 @@
fix_install.patch
hardening+debug_options.patch
fix_reading_fasta.patch
-include_kraken2_headers.patch
=====================================
docs/MANUAL.html
=====================================
@@ -13,7 +13,7 @@
<div class="pretoc">
<p class="title">Kraken taxonomic sequence classification system</p>
- <p class="version">Version 2.1.0</p>
+ <p class="version">Version 2.1.1</p>
<p>Operating Manual</p>
</div>
=====================================
docs/top.html
=====================================
@@ -1,7 +1,7 @@
<div class="pretoc">
<p class="title">Kraken taxonomic sequence classification system</p>
- <p class="version">Version 2.1.0</p>
+ <p class="version">Version 2.1.1</p>
<p>Operating Manual</p>
</div>
=====================================
install_kraken2.sh
=====================================
@@ -6,7 +6,7 @@
set -e
-VERSION="2.1.0"
+VERSION="2.1.1"
if [ -z "$1" ] || [ -n "$2" ]
then
=====================================
scripts/standard_installation.sh
=====================================
@@ -26,7 +26,7 @@ if [ -n "$KRAKEN2_USE_FTP" ]; then
ftp_flag="--use-ftp"
fi
-kraken2-build --db $KRAKEN2_DB_NAME --download-taxonomy --skip-maps $masking_flag $protein_flag $ftp_flag
+kraken2-build --db $KRAKEN2_DB_NAME --download-taxonomy $masking_flag $protein_flag $ftp_flag
kraken2-build --db $KRAKEN2_DB_NAME --download-library archaea $masking_flag $protein_flag $ftp_flag
kraken2-build --db $KRAKEN2_DB_NAME --download-library bacteria $masking_flag $protein_flag $ftp_flag
kraken2-build --db $KRAKEN2_DB_NAME --download-library viral $masking_flag $protein_flag $ftp_flag
=====================================
src/hyperloglogplus.h
=====================================
@@ -5,24 +5,23 @@
*/
/*
- * Implementation of 64-bit HyperLogLog algorithm by Flajolet et al.,
- * with sparse mode for increased precision with low cardinalities (Stefan Heule et al.), and
+ * Implementation of 64-bit HyperLogLog algorithm by Flajolet et al.,
+ * with sparse mode for increased precision with low cardinalities (Stefan Heule et al.), and
* an improved estimator that does not rely on empirical bias correction data (Otmar Ertl)
*/
#ifndef HYPERLOGLOGPLUS_H_
#define HYPERLOGLOGPLUS_H_
-#include<vector>
-#include<unordered_set>
+#include "kraken2_headers.h"
using namespace std;
//#define HLL_DEBUG
//#define HLL_DEBUG2
-#ifdef HLL_DEBUG
+#ifdef HLL_DEBUG
#define D(x) x
-#else
+#else
#define D(x)
#endif
@@ -36,7 +35,7 @@ typedef unordered_set<uint32_t> SparseListType;
// Other possible SparseList types:
// // typedef vector<uint32_t> SparseListType;
// The sorted vector implementation is pretty inefficient currently, as the vector
-// is always kept sorted.
+// is always kept sorted.
// //typedef unordered_set<uint32_t, NoHash<uint32_t> > SparseListType;
// No real performance gain from using the hash value directly - and probably problems
// with the bucket assignment, since unordered_set expects size_t hashes
@@ -59,10 +58,10 @@ private:
HASH (*bit_mixer) (uint64_t);
// sparse versions of p and m
- static const uint8_t pPrime = 25; // precision when using a sparse representation
+ static const uint8_t pPrime = 25; // precision when using a sparse representation
// which encodes the rank + index in 32 bits:
- // 25 bits for index +
- // 6 bits for rank +
+ // 25 bits for index +
+ // 6 bits for rank +
// 1 flag bit indicating if bits p..pPrime are 0
static const uint32_t mPrime = 1 << pPrime; // 2^pPrime
@@ -93,10 +92,10 @@ public:
uint64_t cardinality() const; // returns ertlCardinality()
uint64_t size() const; // returns ertlCardinality()
// HLL++ estimator of Heule et al., 2015. Uses empirical bias correction factors
- uint64_t heuleCardinality(bool correct_bias = true) const;
+ uint64_t heuleCardinality(bool correct_bias = true) const;
// Improved estimator of Ertl, 2017. Does not rely on empirical data
uint64_t ertlCardinality() const;
- // Flayolet's cardinality estimator without bias correction
+ // Flajolet's cardinality estimator without bias correction
uint64_t flajoletCardinality(bool use_sparse_precision = true) const;
uint64_t nObserved() const;
@@ -108,4 +107,3 @@ private:
};
#endif /* HYPERLOGLOGPLUS_H_ */
-
View it on GitLab: https://salsa.debian.org/med-team/kraken2/-/compare/54954f543bdf7da3eb0a7be889517f5c289372da...c019d9051507454e73a19a8751e4486252510f26
--
View it on GitLab: https://salsa.debian.org/med-team/kraken2/-/compare/54954f543bdf7da3eb0a7be889517f5c289372da...c019d9051507454e73a19a8751e4486252510f26
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