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1.2
date	2023.08.29.21.49.57;	author bacon;	state Exp;
branches;
next	1.1;
commitid	3t5B44MuRw1jiJCE;

1.1
date	2023.07.31.14.34.18;	author bacon;	state Exp;
branches;
next	;
commitid	qOkQl0Djtm2EOXyE;


desc
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1.2
log
@biology/rna-star: Fix build on Darwin 21.6.0 x86

Remove extern "C" in file build with c++
@
text
@$NetBSD$

# Portability

--- bamSortByCoordinate.cpp.orig	2022-11-01 14:50:35.000000000 +0000
+++ bamSortByCoordinate.cpp
@@@@ -69,7 +69,7 @@@@ void bamSortByCoordinate (Parameters &P,
                             boolWait=false;
                             totalMem+=newMem;
                         };
-                        sleep(0.1);
+                        usleep(100000);
                     };
                     BAMbinSortByCoordinate(ibin,binN,binS,P.runThreadN,P.outBAMsortTmpDir, P, genome, solo);
                     #pragma omp critical
@


1.1
log
@biology/rna-star: Spliced Transcripts Align to a Ref

STAR (Spliced Transcripts Alignment to a Reference) aims to achieve
accurate alignment of high-throughput RNA-seq data.  STAR is based on
a previously undescribed RNA-seq alignment algorithm that uses
sequential maximum mappable seed search in uncompressed suffix arrays
followed by seed clustering and stitching procedure. STAR outperforms
other aligners by a factor of >50 in mapping speed, aligning to the
human genome 550 million 2 x 76 bp paired-end reads per hour on a modest
12-core server, while at the same time improving alignment sensitivity
and precision.
@
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