biology/subread: Read alignment, quantification and mutation discovery

The Subread package comprises a suite of software programs for processing
next-gen sequencing read data including:

    Subread: a general-purpose read aligner
    Subjunc: a read aligner developed for aligning RNA-seq reads
    featureCounts: a software program developed for counting reads to genomic
    features such as genes, exons, promoters and genomic bins.
    Sublong: a long-read aligner that is designed based on seed-and-vote.
    exactSNP: discovers SNPs by testing signals against local background noise.

1 files changed, 37 insertions, 0 deletions

diff --git a/biology/subread/files/patch-longread-one_longread-mapping.c b/biology/subread/files/patch-longread-one_longread-mapping.c
new file mode 100644
index 000000000000..d1304ef7d4d8
--- /dev/null
+++ b/biology/subread/files/patch-longread-one_longread-mapping.c
@@ -0,0 +1,37 @@
+--- longread-one/longread-mapping.c.orig	2019-09-04 04:22:49 UTC
++++ longread-one/longread-mapping.c
+@@ -30,7 +30,9 @@
+ #ifndef __MINGW32__
+ #include <sys/resource.h>
+ #endif
++#ifndef __FreeBSD__	// Deprecated on FreeBSD
+ #include <sys/timeb.h>
++#endif
+ #include <sys/stat.h>
+ #include <locale.h>
+ #include <ctype.h>
+@@ -223,9 +225,24 @@ int LRMvalidate_and_init_context(LRMcontext_t ** conte
+ 
+ double LRMmiltime(){
+ 	double ret;
++
++/* Why not use gettimeofday() on all platforms? */
++#ifdef __FreeBSD__
++
++	struct timeval tp;
++	struct timezone tz;
++	tz.tz_minuteswest=0;
++	tz.tz_dsttime=0;
++	gettimeofday(&tp,&tz);
++	ret = tp.tv_sec+ 0.001*0.001* tp.tv_usec; 
++
++#else
++
+ 	struct timeb trp;
+ 	ftime(&trp);
+ 	ret = trp.time*1.0+(trp.millitm*1.0/1000.0);
++
++#endif
+ 	return ret;
+ }
+