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 <npatra...@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 <npatra...@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 You're receiving this email because of your account on salsa.debian.org.
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