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