gnu: bedtools: Update to 2.25.0.
* gnu/packages/bioinformatics.scm (bedtools): Update to 0.25.0. [source]: Remove patch merged upstream. [arguments]: Use 'modify-phases'. Remove 'patch-makefile-SHELL-definition' phase. * gnu/packages/patches/bedtools-32bit-compilation.patch: Remove file. * gnu-system.am (dist_patch_DATA): Remove it.
This commit is contained in:
Ben Woodcroft
parent
6573ac82ad
commit
9b9b7ffd8e
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@ -416,7 +416,6 @@ dist_patch_DATA = \
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gnu/packages/patches/avidemux-install-to-lib.patch \
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gnu/packages/patches/avrdude-fix-libusb.patch \
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gnu/packages/patches/bash-completion-directories.patch \
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gnu/packages/patches/bedtools-32bit-compilation.patch \
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gnu/packages/patches/bowtie-fix-makefile.patch \
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gnu/packages/patches/bigloo-gc-shebangs.patch \
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gnu/packages/patches/binutils-ld-new-dtags.patch \
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@ -1,6 +1,6 @@
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;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2014, 2015 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2015 Ben Woodcroft <donttrustben@gmail.com>
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;;; Copyright © 2015, 2016 Ben Woodcroft <donttrustben@gmail.com>
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;;; Copyright © 2015 Pjotr Prins <pjotr.guix@thebird.nl>
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;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
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;;;
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@ -207,7 +207,7 @@ computational cluster.")
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(define-public bedtools
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(package
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(name "bedtools")
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(version "2.24.0")
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(version "2.25.0")
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(source (origin
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(method url-fetch)
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(uri (string-append "https://github.com/arq5x/bedtools2/archive/v"
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@ -215,8 +215,7 @@ computational cluster.")
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(file-name (string-append name "-" version ".tar.gz"))
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(sha256
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(base32
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"0lnxrjvs3nnmb4bmskag1wg3h2hd80przz5q3xd0bvs7vyxrvpbl"))
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(patches (list (search-patch "bedtools-32bit-compilation.patch")))))
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"1ywcy3yfwzhl905b51l0ffjia55h75vv3mw5xkvib04pp6pj548m"))))
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(build-system gnu-build-system)
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(native-inputs `(("python" ,python-2)))
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(inputs `(("samtools" ,samtools)
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@ -225,16 +224,6 @@ computational cluster.")
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'(#:test-target "test"
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'patch-makefile-SHELL-definition
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(lambda _
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;; patch-makefile-SHELL cannot be used here as it does not
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;; yet patch definitions with `:='. Since changes to
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;; patch-makefile-SHELL result in a full rebuild, features
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;; of patch-makefile-SHELL are reimplemented here.
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(substitute* "Makefile"
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(("^SHELL := .*$")
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(string-append "SHELL := " (which "bash") " -e \n")))
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#t))
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(delete 'configure)
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(replace 'install
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(lambda* (#:key outputs #:allow-other-keys)
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@ -1,171 +0,0 @@
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Fixed in upstream, see
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https://github.com/arq5x/bedtools2/issues/271
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From b47dbefcb57f8e6c4fe397f64346338620740b71 Mon Sep 17 00:00:00 2001
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From: arq5x <arq5x@virginia.edu>
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Date: Wed, 15 Jul 2015 15:15:23 -0600
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Subject: [PATCH] settle on uint32_t signature for QuickString. Resolves #267
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and #271?
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---
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src/coverageFile/coverageFile.cpp | 24 ++++++++++++------------
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src/utils/general/QuickString.cpp | 27 ++++++++++++++-------------
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src/utils/general/QuickString.h | 6 +++---
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3 files changed, 29 insertions(+), 28 deletions(-)
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diff --git a/src/coverageFile/coverageFile.cpp b/src/coverageFile/coverageFile.cpp
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index 859cfdc..0fb544b 100644
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--- a/src/coverageFile/coverageFile.cpp
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+++ b/src/coverageFile/coverageFile.cpp
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@@ -83,11 +83,11 @@ void CoverageFile::giveFinalReport(RecordOutputMgr *outputMgr) {
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float depthPct = (float)basesAtDepth / (float)_totalQueryLen;
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_finalOutput = "all\t";
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- _finalOutput.append(depth);
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+ _finalOutput.append(static_cast<uint32_t>(depth));
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_finalOutput.append("\t");
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- _finalOutput.append(basesAtDepth);
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+ _finalOutput.append(static_cast<uint32_t>(basesAtDepth));
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_finalOutput.append("\t");
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- _finalOutput.append(_totalQueryLen);
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+ _finalOutput.append(static_cast<uint32_t>(_totalQueryLen));
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_finalOutput.append("\t");
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format(depthPct);
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@@ -138,7 +138,7 @@ size_t CoverageFile::countBasesAtDepth(size_t depth) {
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void CoverageFile::doCounts(RecordOutputMgr *outputMgr, RecordKeyVector &hits)
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{
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- _finalOutput = hits.size();
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+ _finalOutput = static_cast<uint32_t>(hits.size());
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outputMgr->printRecord(hits.getKey(), _finalOutput);
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}
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@@ -147,9 +147,9 @@ void CoverageFile::doPerBase(RecordOutputMgr *outputMgr, RecordKeyVector &hits)
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//loop through all bases in query, printing full record and metrics for each
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const Record * queryRec = hits.getKey();
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for (size_t i= 0; i < _queryLen; i++) {
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- _finalOutput = i +1;
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+ _finalOutput = static_cast<uint32_t>(i+1);
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_finalOutput.append("\t");
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- _finalOutput.append(_depthArray[i]);
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+ _finalOutput.append(static_cast<uint32_t>(_depthArray[i]));
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outputMgr->printRecord(queryRec, _finalOutput);
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}
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@@ -181,11 +181,11 @@ void CoverageFile::doHist(RecordOutputMgr *outputMgr, RecordKeyVector &hits)
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size_t numBasesAtDepth = iter->second;
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float coveredBases = (float)numBasesAtDepth / (float)_queryLen;
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- _finalOutput = depth;
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+ _finalOutput = static_cast<uint32_t>(depth);
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_finalOutput.append("\t");
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- _finalOutput.append(numBasesAtDepth);
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+ _finalOutput.append(static_cast<uint32_t>(numBasesAtDepth));
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_finalOutput.append("\t");
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- _finalOutput.append(_queryLen);
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+ _finalOutput.append(static_cast<uint32_t>(_queryLen));
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_finalOutput.append("\t");
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format(coveredBases);
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@@ -199,11 +199,11 @@ void CoverageFile::doDefault(RecordOutputMgr *outputMgr, RecordKeyVector &hits)
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size_t nonZeroBases = _queryLen - countBasesAtDepth(0);
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float coveredBases = (float)nonZeroBases / (float)_queryLen;
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- _finalOutput = hits.size();
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+ _finalOutput = static_cast<uint32_t>(hits.size());
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_finalOutput.append("\t");
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- _finalOutput.append(nonZeroBases);
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+ _finalOutput.append(static_cast<uint32_t>(nonZeroBases));
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_finalOutput.append("\t");
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- _finalOutput.append(_queryLen);
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+ _finalOutput.append(static_cast<uint32_t>(_queryLen));
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_finalOutput.append("\t");
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format(coveredBases);
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diff --git a/src/utils/general/QuickString.cpp b/src/utils/general/QuickString.cpp
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index 0757009..a83263e 100644
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--- a/src/utils/general/QuickString.cpp
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+++ b/src/utils/general/QuickString.cpp
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@@ -105,11 +105,11 @@ QuickString &QuickString::operator = (uint32_t val) {
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return *this;
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}
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-QuickString &QuickString::operator = (size_t val) {
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- clear();
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- append(val);
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- return *this;
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-}
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+// QuickString &QuickString::operator = (size_t val) {
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+// clear();
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+// append(val);
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+// return *this;
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+// }
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QuickString &QuickString::operator = (float val) {
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clear();
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@@ -158,10 +158,11 @@ QuickString &QuickString::operator += (uint32_t num) {
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return *this;
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}
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-QuickString &QuickString::operator += (size_t num) {
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- append(num);
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- return *this;
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-}
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+// QuickString &QuickString::operator += (size_t num) {
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+// append(num);
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+// return *this;
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+// }
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+
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QuickString &QuickString::operator += (float num) {
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append(num);
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return *this;
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@@ -273,12 +274,12 @@ void QuickString::append(int num) {
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}
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void QuickString::append(uint32_t num) {
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- int2str((int)num, *this, true);
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+ int2str((int)num, *this, true);
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}
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-void QuickString::append(size_t num) {
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- int2str((int)num, *this, true);
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-}
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+// void QuickString::append(size_t num) {
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+// int2str((int)num, *this, true);
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+// }
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void QuickString::append(float num) {
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append(ToString(num));
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diff --git a/src/utils/general/QuickString.h b/src/utils/general/QuickString.h
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index b43fdfc..6e6fa94 100644
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--- a/src/utils/general/QuickString.h
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+++ b/src/utils/general/QuickString.h
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@@ -38,7 +38,7 @@ class QuickString {
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QuickString &operator = (char);
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QuickString &operator = (int);
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QuickString &operator = (uint32_t);
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- QuickString &operator = (size_t);
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+ //QuickString &operator = (size_t);
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QuickString &operator = (float);
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QuickString &operator = (double);
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QuickString &operator += (const QuickString &);
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@@ -47,7 +47,7 @@ class QuickString {
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QuickString &operator += (char);
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QuickString &operator += (int);
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QuickString &operator += (uint32_t);
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- QuickString &operator += (size_t);
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+ //QuickString &operator += (size_t);
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QuickString &operator += (float);
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QuickString &operator += (double);
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@@ -74,7 +74,7 @@ class QuickString {
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//for better performance.
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void append(int num);
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void append(uint32_t num);
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- void append(size_t num);
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+ //void append(size_t num);
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void append(float num);
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void append(double num);
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