Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 537981) +++ head/biology/Makefile (revision 537982) @@ -1,179 +1,180 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += abyss SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools SUBDIR += biococoa SUBDIR += bolt-lmm SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += checkm SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += cufflinks SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += dsr-pdb SUBDIR += emboss SUBDIR += exonerate SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastp SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += figtree SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gcta SUBDIR += gemma SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += graphlan SUBDIR += grappa SUBDIR += groopm SUBDIR += haplohseq SUBDIR += hhsuite SUBDIR += hisat2 SUBDIR += hmmer SUBDIR += htslib SUBDIR += hyphy SUBDIR += igv SUBDIR += infernal SUBDIR += iolib SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish SUBDIR += kallisto SUBDIR += lagan SUBDIR += lamarc SUBDIR += libbigwig SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += minimap2 SUBDIR += molden SUBDIR += mopac SUBDIR += mothur SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit SUBDIR += ncbi-toolkit SUBDIR += ngs-sdk SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Cluster SUBDIR += p5-Bio-Coordinate SUBDIR += p5-Bio-DB-EMBL SUBDIR += p5-Bio-DB-NCBIHelper SUBDIR += p5-Bio-Das SUBDIR += p5-Bio-Das-Lite SUBDIR += p5-Bio-FeatureIO SUBDIR += p5-Bio-GFF3 SUBDIR += p5-Bio-Glite SUBDIR += p5-Bio-Graphics SUBDIR += p5-Bio-MAGETAB SUBDIR += p5-Bio-NEXUS SUBDIR += p5-Bio-Phylo SUBDIR += p5-Bio-SCF SUBDIR += p5-Bio-Variation SUBDIR += p5-BioPerl SUBDIR += p5-BioPerl-Run SUBDIR += p5-TrimGalore SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += pbbam SUBDIR += pbcopper SUBDIR += pbseqan SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += plink SUBDIR += primer3 SUBDIR += prodigal SUBDIR += prodigy-lig SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-dnaio SUBDIR += py-ete3 SUBDIR += py-fastTSNE SUBDIR += py-gffutils SUBDIR += py-gtfparse SUBDIR += py-hits SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-multiqc SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pandas-charm SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-scikit-bio SUBDIR += py-xenaPython SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools SUBDIR += scrm SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtk SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += stacks SUBDIR += star SUBDIR += stringtie + SUBDIR += subread SUBDIR += tRNAscan-SE SUBDIR += tabixpp SUBDIR += tophat SUBDIR += treekin SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += viennarna SUBDIR += vsearch SUBDIR += vt SUBDIR += wise .include Index: head/biology/subread/Makefile =================================================================== --- head/biology/subread/Makefile (nonexistent) +++ head/biology/subread/Makefile (revision 537982) @@ -0,0 +1,23 @@ +# $FreeBSD$ + +PORTNAME= subread +DISTVERSION= 2.0.1 +DISTVERSIONSUFFIX= -source +CATEGORIES= biology +MASTER_SITES= SF/${PORTNAME}/${PORTNAME}-${PORTVERSION} + +MAINTAINER= jwb@FreeBSD.org +COMMENT= High-performance read alignment, quantification and mutation discovery + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKDIR}/${DISTNAME}/LICENSE + +LIB_DEPENDS= libsysinfo.so:devel/libsysinfo + +USES= gmake localbase:ldflags + +MAKEFILE= ${FILESDIR}/Makefile.pkg +WRKSRC_SUBDIR= src +INSTALL_TARGET= install-strip + +.include Property changes on: head/biology/subread/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/subread/distinfo =================================================================== --- head/biology/subread/distinfo (nonexistent) +++ head/biology/subread/distinfo (revision 537982) @@ -0,0 +1,3 @@ +TIMESTAMP = 1591305316 +SHA256 (subread-2.0.1-source.tar.gz) = d808eb5b1823c572cb45a97c95a3c5acb3d8e29aa47ec74e3ca1eb345787c17b +SIZE (subread-2.0.1-source.tar.gz) = 23260381 Property changes on: head/biology/subread/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/subread/files/Makefile.pkg =================================================================== --- head/biology/subread/files/Makefile.pkg (nonexistent) +++ head/biology/subread/files/Makefile.pkg (revision 537982) @@ -0,0 +1,104 @@ + + +include makefile.version + +CCFLAGS = -DMAKE_FOR_EXON -DMAKE_STANDALONE \ + -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" -D_FILE_OFFSET_BITS=64 +LDFLAGS += -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm +CC ?= gcc +CC += ${CCFLAGS} + +BINS = detectionCall sublong repair txUnique featureCounts removeDup \ + exactSNP subread-buildindex subindel subread-align subjunc \ + qualityScores subread-fullscan propmapped flattenGTF \ + +MKDIR ?= mkdir -p +INSTALL ?= install +DESTDIR ?= . +PREFIX ?= local +STRIP ?= strip + +ALL_LIBS= core core-junction core-indel sambam-file sublog gene-algorithms hashtable input-files sorted-hashtable gene-value-index exon-algorithms HelperFunctions interval_merge long-hashtable core-bigtable seek-zlib input-blc +ALL_OBJECTS=$(addsuffix .o, ${ALL_LIBS}) +ALL_H=$(addsuffix .h, ${ALL_LIBS}) +ALL_C=$(addsuffix .c, ${ALL_LIBS}) + +all: genRandomReads detectionCall sublong repair txUnique featureCounts removeDup exactSNP subread-buildindex subindel subread-align subjunc qualityScores subread-fullscan propmapped flattenGTF # samMappedBases mergeVCF testZlib + mkdir -p ../bin/utilities + mv longread-one/LRM longread-one/sublong + mv longread-one/sublong subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/ + mv detectionCall genRandomReads repair propmapped qualityScores removeDup subread-fullscan txUnique flattenGTF ../bin/utilities + +sublong: longread-one/longread-mapping.c ${ALL_OBJECTS} + echo " " > longread-one/make.version + rm -f longread-one/*.o + cd longread-one && $(MAKE) + +genRandomReads: gen_rand_reads.c ${ALL_OBJECTS} + ${CC} -o genRandomReads gen_rand_reads.c ${ALL_OBJECTS} ${LDFLAGS} + +flattenGTF: flattenAnnotations.c ${ALL_OBJECTS} + ${CC} -o flattenGTF flattenAnnotations.c ${ALL_OBJECTS} ${LDFLAGS} + +detectionCall: detection-calls.c ${ALL_OBJECTS} + ${CC} -o detectionCall detection-calls.c ${ALL_OBJECTS} ${LDFLAGS} + +repair: read-repair.c ${ALL_OBJECTS} + ${CC} -o repair read-repair.c ${ALL_OBJECTS} ${LDFLAGS} + +txUnique: tx-unique.c tx-unique.h ${ALL_OBJECTS} + ${CC} -o txUnique tx-unique.c ${ALL_OBJECTS} ${LDFLAGS} + +globalReassembly: global-reassembly.c ${ALL_OBJECTS} + ${CC} -o globalReassembly global-reassembly.c ${ALL_OBJECTS} ${LDFLAGS} + +propmapped: propmapped.c ${ALL_OBJECTS} + ${CC} -o propmapped propmapped.c ${ALL_OBJECTS} ${LDFLAGS} + +exactSNP: SNPCalling.c SNPCalling.h ${ALL_OBJECTS} + ${CC} -o exactSNP SNPCalling.c ${ALL_OBJECTS} ${LDFLAGS} + +subread-buildindex: index-builder.c subread.h ${ALL_OBJECTS} + ${CC} -o subread-buildindex index-builder.c ${ALL_OBJECTS} ${LDFLAGS} + +removeDup: removeDupReads.c removeDupReads.h subread.h ${ALL_OBJECTS} + ${CC} -o removeDup removeDupReads.c ${ALL_OBJECTS} ${LDFLAGS} + +subindel: SUBindel.c core.h subread.h ${ALL_OBJECTS} + ${CC} -o subindel SUBindel.c ${ALL_OBJECTS} ${LDFLAGS} + +featureCounts: readSummary.c subread.h ${ALL_OBJECTS} + ${CC} -o featureCounts readSummary.c ${ALL_OBJECTS} ${LDFLAGS} + +subread-align: core-interface-aligner.c ${ALL_OBJECTS} + ${CC} -o subread-align core-interface-aligner.c ${ALL_OBJECTS} ${LDFLAGS} + +subjunc: core-interface-subjunc.c ${ALL_OBJECTS} + ${CC} -o subjunc core-interface-subjunc.c ${ALL_OBJECTS} ${LDFLAGS} + +subtools: subtools.c ${ALL_OBJECTS} + ${CC} -o subtools subtools.c ${ALL_OBJECTS} ${LDFLAGS} + +qualityScores: qualityScores.c ${ALL_OBJECTS} + ${CC} -o qualityScores qualityScores.c ${ALL_OBJECTS} ${LDFLAGS} + +subread-fullscan: fullscan.c ${ALL_OBJECTS} + ${CC} -o subread-fullscan fullscan.c ${ALL_OBJECTS} ${LDFLAGS} + +.PHONY: clean install install-strip + +install-strip: install + ${STRIP} ${DESTDIR}${PREFIX}/bin/* + +install: + ${MKDIR} ${DESTDIR}${PREFIX}/bin + ${INSTALL} -c \ + ../bin/exactSNP \ + ../bin/featureCounts \ + ../bin/sub* \ + ../bin/utilities/* \ + ${DESTDIR}${PREFIX}/bin + +clean: + rm -f core featureCounts exactSNP removeDup subread-buildindex \ + ${ALL_OBJECTS} Property changes on: head/biology/subread/files/Makefile.pkg ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/subread/files/patch-HelperFunctions.c =================================================================== --- head/biology/subread/files/patch-HelperFunctions.c (nonexistent) +++ head/biology/subread/files/patch-HelperFunctions.c (revision 537982) @@ -0,0 +1,20 @@ +--- HelperFunctions.c.orig 2020-06-04 23:58:40 UTC ++++ HelperFunctions.c +@@ -845,7 +845,7 @@ int strcmp_number(char * s1, char * s2) + + int mac_str(char * str_buff) + { +-#if defined(FREEBSD) || defined(__MINGW32__) ++#if defined(__FreeBSD__) || defined(__MINGW32__) + return 1; + #else + #ifdef MACOS +@@ -2703,7 +2703,7 @@ void main(){ + + int get_free_total_mem(size_t * total, size_t * free_mem){ + +-#ifdef FREEBSD ++#ifdef __FreeBSD__ + return -1; + #endif + Property changes on: head/biology/subread/files/patch-HelperFunctions.c ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/subread/files/patch-core-junction.c =================================================================== --- head/biology/subread/files/patch-core-junction.c (nonexistent) +++ head/biology/subread/files/patch-core-junction.c (revision 537982) @@ -0,0 +1,10 @@ +--- core-junction.c.orig 2018-11-08 15:19:02 UTC ++++ core-junction.c +@@ -22,6 +22,7 @@ + #include + #include + #include ++#include + #include "subread.h" + #include "sublog.h" + #include "gene-value-index.h" Property changes on: head/biology/subread/files/patch-core-junction.c ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/subread/files/patch-gene-algorithms.c =================================================================== --- head/biology/subread/files/patch-gene-algorithms.c (nonexistent) +++ head/biology/subread/files/patch-gene-algorithms.c (revision 537982) @@ -0,0 +1,20 @@ +--- gene-algorithms.c.orig 2020-06-04 23:57:31 UTC ++++ gene-algorithms.c +@@ -28,7 +28,7 @@ + #include + #include + +-#ifndef FREEBSD ++#ifndef __FreeBSD__ + #include + #endif + +@@ -1563,7 +1563,7 @@ int load_offsets(gene_offset_t* offsets , const char i + + double miltime(){ + double ret; +- #ifdef FREEBSD ++ #ifdef __FreeBSD__ + struct timeval tp; + struct timezone tz; + tz.tz_minuteswest=0; Property changes on: head/biology/subread/files/patch-gene-algorithms.c ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/subread/files/patch-input-files.c =================================================================== --- head/biology/subread/files/patch-input-files.c (nonexistent) +++ head/biology/subread/files/patch-input-files.c (revision 537982) @@ -0,0 +1,11 @@ +--- input-files.c.orig 2020-06-05 00:33:03 UTC ++++ input-files.c +@@ -48,7 +48,7 @@ FILE * f_subr_open(const char * fname, const char * mo + #ifdef __MINGW32__ + return fopen64(fname, mode); + #else +-#if defined(__LP64__) || defined(_LP64) || defined(MACOS) ++#if defined(__LP64__) || defined(_LP64) || defined(MACOS) || defined(__FreeBSD__) + return fopen(fname, mode); + #else + return fopen64(fname, mode); Property changes on: head/biology/subread/files/patch-input-files.c ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/subread/files/patch-long-hashtable.c =================================================================== --- head/biology/subread/files/patch-long-hashtable.c (nonexistent) +++ head/biology/subread/files/patch-long-hashtable.c (revision 537982) @@ -0,0 +1,11 @@ +--- long-hashtable.c.orig 2020-06-04 23:59:33 UTC ++++ long-hashtable.c +@@ -22,7 +22,7 @@ + #include + + #ifndef MACOS +-#ifndef FREEBSD ++#ifndef __FreeBSD__ + #include + #endif + #endif Property changes on: head/biology/subread/files/patch-long-hashtable.c ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/subread/files/patch-longread-one_LRMsorted-hashtable.c =================================================================== --- head/biology/subread/files/patch-longread-one_LRMsorted-hashtable.c (nonexistent) +++ head/biology/subread/files/patch-longread-one_LRMsorted-hashtable.c (revision 537982) @@ -0,0 +1,15 @@ +--- longread-one/LRMsorted-hashtable.c.orig 2018-11-08 14:47:43 UTC ++++ longread-one/LRMsorted-hashtable.c +@@ -22,11 +22,9 @@ + #include + #include "LRMsorted-hashtable.h" + +-#ifndef MACOS +-#ifndef FREEBSD ++#if !defined(__APPLE__) && !defined(__FreeBSD__) + #include + #endif +-#endif + + #include + #include "LRMfile-io.h" Property changes on: head/biology/subread/files/patch-longread-one_LRMsorted-hashtable.c ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/subread/files/patch-longread-one_Makefile =================================================================== --- head/biology/subread/files/patch-longread-one_Makefile (nonexistent) +++ head/biology/subread/files/patch-longread-one_Makefile (revision 537982) @@ -0,0 +1,30 @@ +--- longread-one/Makefile.orig 2019-09-04 04:22:49 UTC ++++ longread-one/Makefile +@@ -1,12 +1,12 @@ +-CC_EXEC = gcc + OPT_LEVEL = 3 + + include ../makefile.version + include make.version + +-CCFLAGS = -mtune=core2 ${MACOS} -O${OPT_LEVEL} -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" ${WARNING_LEVEL} ${MINGW32} +-LDFLAGS = -lpthread -lz -lm -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST +-CC = ${CC_EXEC} ${CCFLAGS} -fmessage-length=0 -ggdb ++CC ?= gcc ++CFLAGS += -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 \ ++ -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" ${WARNING_LEVEL} ${MINGW32} ++LDFLAGS += -lpthread -lz -lm -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST + + ALL_LIBS=LRMsorted-hashtable LRMbase-index LRMchro-event LRMhelper LRMseek-zlib LRMfile-io LRMhashtable + ALL_OBJECTS=$(addsuffix .o, ${ALL_LIBS}) +@@ -20,8 +20,8 @@ clean: + rm -f *.o LRM + + LRM: longread-mapping.c ${ALL_OBJECTS} +- ${CC} -o LRM longread-mapping.c ${ALL_OBJECTS} ${LDFLAGS} ++ ${CC} -o LRM ${CFLAGS} longread-mapping.c ${ALL_OBJECTS} ${LDFLAGS} + + $(ALL_OBJECTS): $(ALL_C) $(ALL_H) +- $(CC) -o $@ -c $(subst .o,.c,$@) ++ $(CC) -o $@ -c ${CFLAGS} $(subst .o,.c,$@) + Property changes on: head/biology/subread/files/patch-longread-one_Makefile ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/subread/files/patch-longread-one_longread-mapping.c =================================================================== --- head/biology/subread/files/patch-longread-one_longread-mapping.c (nonexistent) +++ head/biology/subread/files/patch-longread-one_longread-mapping.c (revision 537982) @@ -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 + #endif ++#ifndef __FreeBSD__ // Deprecated on FreeBSD + #include ++#endif + #include + #include + #include +@@ -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; + } + Property changes on: head/biology/subread/files/patch-longread-one_longread-mapping.c ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/subread/files/patch-read-repair.c =================================================================== --- head/biology/subread/files/patch-read-repair.c (nonexistent) +++ head/biology/subread/files/patch-read-repair.c (revision 537982) @@ -0,0 +1,10 @@ +--- read-repair.c.orig 2018-11-08 15:20:06 UTC ++++ read-repair.c +@@ -3,6 +3,7 @@ + #include + #include + #include ++#include + #include "subread.h" + #include "core.h" + #include "input-files.h" Property changes on: head/biology/subread/files/patch-read-repair.c ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/subread/files/patch-sambam-file.c =================================================================== --- head/biology/subread/files/patch-sambam-file.c (nonexistent) +++ head/biology/subread/files/patch-sambam-file.c (revision 537982) @@ -0,0 +1,10 @@ +--- sambam-file.c.orig 2018-11-08 15:20:35 UTC ++++ sambam-file.c +@@ -30,6 +30,7 @@ + #include + #include + #include ++#include + #include "subread.h" + #include "core.h" + #include "gene-algorithms.h" Property changes on: head/biology/subread/files/patch-sambam-file.c ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/subread/files/patch-sorted-hashtable.c =================================================================== --- head/biology/subread/files/patch-sorted-hashtable.c (nonexistent) +++ head/biology/subread/files/patch-sorted-hashtable.c (revision 537982) @@ -0,0 +1,15 @@ +--- sorted-hashtable.c.orig 2018-11-08 03:33:50 UTC ++++ sorted-hashtable.c +@@ -23,11 +23,9 @@ + #include + #include + +-#ifndef MACOS +-#ifndef FREEBSD ++#if !defined(__FreeBSD__) && !defined(__APPLE__) + #include + #endif +-#endif + + #include + #include"core.h" Property changes on: head/biology/subread/files/patch-sorted-hashtable.c ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/subread/files/patch-subread.h =================================================================== --- head/biology/subread/files/patch-subread.h (nonexistent) +++ head/biology/subread/files/patch-subread.h (revision 537982) @@ -0,0 +1,11 @@ +--- subread.h.orig 2018-11-08 14:46:06 UTC ++++ subread.h +@@ -102,7 +102,7 @@ + + #define USE_POSIX_MUTEX_LOCK + +-#if defined(MACOS) || defined(FREEBSD) || defined(USE_POSIX_MUTEX_LOCK) ++#if defined(__APPLE__) || defined(__FreeBSD__) || defined(USE_POSIX_MUTEX_LOCK) + typedef pthread_mutex_t subread_lock_t; + #define pthread_spinlock_t pthread_mutex_t + #define pthread_spin_lock pthread_mutex_lock Property changes on: head/biology/subread/files/patch-subread.h ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/subread/pkg-descr =================================================================== --- head/biology/subread/pkg-descr (nonexistent) +++ head/biology/subread/pkg-descr (revision 537982) @@ -0,0 +1,20 @@ +The Subread package comprises a suite of software programs for processing +next-gen sequencing read data including: + + Subread: a general-purpose read aligner which can align both genomic + DNA-seq and RNA-seq reads. It can also be used to discover genomic + mutations including short indels and structural variants. + + Subjunc: a read aligner developed for aligning RNA-seq reads and for the + detection of exon-exon junctions. Gene fusion events can be detected as + well. + + 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: a SNP caller that discovers SNPs by testing signals against local + background noises. + +WWW: http://bioinf.wehi.edu.au/subread-package/ Property changes on: head/biology/subread/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/subread/pkg-plist =================================================================== --- head/biology/subread/pkg-plist (nonexistent) +++ head/biology/subread/pkg-plist (revision 537982) @@ -0,0 +1,16 @@ +bin/detectionCall +bin/exactSNP +bin/featureCounts +bin/flattenGTF +bin/genRandomReads +bin/propmapped +bin/qualityScores +bin/removeDup +bin/repair +bin/subindel +bin/subjunc +bin/sublong +bin/subread-align +bin/subread-buildindex +bin/subread-fullscan +bin/txUnique Property changes on: head/biology/subread/pkg-plist ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property