<pre style='margin:0'>
Marcus Calhoun-Lopez (MarcusCalhoun-Lopez) pushed a commit to branch master
in repository macports-ports.
</pre>
<p><a href="https://github.com/macports/macports-ports/commit/3ddfcb2449d2be8133c56bb4ebfd883344a3f1e2">https://github.com/macports/macports-ports/commit/3ddfcb2449d2be8133c56bb4ebfd883344a3f1e2</a></p>
<pre style="white-space: pre; background: #F8F8F8"><span style='display:block; white-space:pre;color:#808000;'>commit 3ddfcb2449d2be8133c56bb4ebfd883344a3f1e2
</span>Author: Marcus Calhoun-Lopez <mcalhoun@macports.org>
AuthorDate: Sat Aug 10 07:14:23 2019 -0700
<span style='display:block; white-space:pre;color:#404040;'> bowtie: update version 1.2.2_p1->1.2.3
</span>---
science/bowtie/Portfile | 10 +++++-----
science/bowtie/files/patch-seqan.diff | 14 +++++++-------
2 files changed, 12 insertions(+), 12 deletions(-)
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/bowtie/Portfile b/science/bowtie/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 35c014d..caff697 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/bowtie/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/bowtie/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -3,8 +3,8 @@
</span> PortSystem 1.0
PortGroup github 1.0
<span style='display:block; white-space:pre;background:#ffe0e0;'>-github.setup BenLangmead bowtie 1.2.2_p1 v
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-revision 2
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+github.setup BenLangmead bowtie 1.2.3 v
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+revision 0
</span> categories science biology
platforms darwin
maintainers {mcalhoun @MarcusCalhoun-Lopez} openmaintainer
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -21,9 +21,9 @@ long_description Bowtie is ${description}. It aligns short DNA sequences
</span>
homepage http://bowtie-bio.sourceforge.net/
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums rmd160 9f818e1e85abaf09ddc58cbe96f9cf735f0ca918 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- sha256 ed1581d6ed97271e6de2c1f826a3169f1d5495461cd6f31b2b8f02e5e4adeebf \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>- size 7890653
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums rmd160 a09f5d4dd685619ab60eef70b08c3b9d376bf85a \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ sha256 9a62e7959a11aa2229722e20800441ce4ecbb2f9e74dd29bd5b2c6f6e4553db8 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ size 7894211
</span>
patchfiles-append patch-Makefile.diff \
patch-seqan.diff
<span style='display:block; white-space:pre;color:#808080;'>diff --git a/science/bowtie/files/patch-seqan.diff b/science/bowtie/files/patch-seqan.diff
</span><span style='display:block; white-space:pre;color:#808080;'>index dca0f99..9ed4f75 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/science/bowtie/files/patch-seqan.diff
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/science/bowtie/files/patch-seqan.diff
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -302,7 +302,7 @@ Last-Update: 2013-04-18
</span> chunkVerbose = false; // have chunk allocator output status messages?
useV1 = true;
reportSe = false;
<span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -1340,7 +1340,7 @@ static void exactSearchWorkerStateful(vo
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1343,7 +1343,7 @@ static void exactSearchWorkerStateful(vo
</span> PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -311,7 +311,7 @@ Last-Update: 2013-04-18
</span> UnpairedExactAlignerV1Factory alSEfact(
ebwt,
NULL,
<span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -1629,7 +1629,7 @@ static void mismatchSearchWorkerFullStat
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1632,7 +1632,7 @@ static void mismatchSearchWorkerFullStat
</span> // Global initialization
PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -320,7 +320,7 @@ Last-Update: 2013-04-18
</span>
Unpaired1mmAlignerV1Factory alSEfact(
ebwtFw,
<span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -2080,7 +2080,7 @@ static void twoOrThreeMismatchSearchWork
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -2083,7 +2083,7 @@ static void twoOrThreeMismatchSearchWork
</span> PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -329,7 +329,7 @@ Last-Update: 2013-04-18
</span> Unpaired23mmAlignerV1Factory alSEfact(
ebwtFw,
&ebwtBw,
<span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -2750,7 +2750,7 @@ static void seededQualSearchWorkerFullSt
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -2753,7 +2753,7 @@ static void seededQualSearchWorkerFullSt
</span> // Global initialization
PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -459,7 +459,7 @@ Last-Update: 2014-08-13
</span>
--- blockwise_sa.h
+++ blockwise_sa.h
<span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -665,8 +665,8 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -673,8 +673,8 @@
</span> try {
// Allocate and initialize containers for holding bucket
// sizes and representatives.
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -470,7 +470,7 @@ Last-Update: 2014-08-13
</span> } catch(bad_alloc &e) {
if(this->_passMemExc) {
throw e; // rethrow immediately
<span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -1055,7 +1055,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1063,7 +1063,7 @@
</span> hi = _sampleSuffs[cur_block];
//zHi.resizeExact(_dcV);
//zHi.fillZero();
<span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -479,7 +479,7 @@ Last-Update: 2014-08-13
</span> assert_eq(getValue(zHi, 0), 0);
calcZ(t, hi, zHi, this->verbose(), this->sanityCheck());
}
<span style='display:block; white-space:pre;background:#ffe0e0;'>-@@ -1066,7 +1066,7 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -1074,7 +1074,7 @@
</span> lo = _sampleSuffs[cur_block-1];
//zLo.resizeExact(_dcV);
//zLo.fillZero();
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