biology/vcflib: Move man pages to share/man

Approved by:	portmgr (blanket)

biology/vcflib/Makefile

@@ -1,6 +1,7 @@
 PORTNAME=		vcflib
 DISTVERSIONPREFIX=	v
 DISTVERSION=		1.0.7
+PORTREVISION=		1
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org

biology/vcflib/files/patch-CMakeLists.txt

@@ -1,6 +1,6 @@
---- CMakeLists.txt.orig	2023-01-29 04:57:02 UTC
+--- CMakeLists.txt.orig	2023-02-07 17:22:46 UTC
 +++ CMakeLists.txt
-@@ -9,7 +9,7 @@
+@@ -9,7 +9,7 @@ project(vcflib)
  cmake_minimum_required(VERSION 3.16)
  project(vcflib)
 
@@ -9,7 +9,7 @@
 
  include(ExternalProject)
  include(FeatureSummary)
-@@ -69,7 +69,7 @@ if(NOT CMAKE_BUILD_TYPE)
+@@ -69,7 +69,7 @@ if (${CMAKE_BUILD_TYPE} MATCHES Release)
  endif()
 
  if (${CMAKE_BUILD_TYPE} MATCHES Release)
@@ -18,3 +18,9 @@
    # set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG") # reset CXX_FLAGS to replace -O3 with -Ofast
  endif()
 
+@@ -570,4 +570,4 @@ install(FILES ${INCLUDES} DESTINATION include)
+
+ install(FILES ${INCLUDES} DESTINATION include)
+
+-install(DIRECTORY ${CMAKE_SOURCE_DIR}/man/ DESTINATION ${CMAKE_INSTALL_PREFIX}/man/man1)
++install(DIRECTORY ${CMAKE_SOURCE_DIR}/man/ DESTINATION ${CMAKE_INSTALL_PREFIX}/share/man/man1)

biology/vcflib/pkg-plist

@@ -159,92 +159,92 @@ include/veclib_types.h
 lib/libvcflib.a
 %%ZIG%%lib/libzig.a
 lib/pyvcflib%%PYTHON_EXT_SUFFIX%%.so
-man/man1/abba-baba.1.gz
-man/man1/bFst.1.gz
-man/man1/dumpContigsFromHeader.1.gz
-man/man1/genotypeSummary.1.gz
-man/man1/hapLrt.1.gz
-man/man1/iHS.1.gz
-man/man1/meltEHH.1.gz
-man/man1/normalize-iHS.1.gz
-man/man1/pFst.1.gz
-man/man1/pVst.1.gz
-man/man1/permuteGPAT++.1.gz
-man/man1/permuteSmooth.1.gz
-man/man1/plotHaps.1.gz
-man/man1/popStats.1.gz
-man/man1/pyvcflib.1.gz
-man/man1/segmentFst.1.gz
-man/man1/segmentIhs.1.gz
-man/man1/sequenceDiversity.1.gz
-man/man1/smoother.1.gz
-man/man1/vcf2dag.1.gz
-man/man1/vcf2fasta.1.gz
-man/man1/vcf2tsv.1.gz
-man/man1/vcfaddinfo.1.gz
-man/man1/vcfafpath.1.gz
-man/man1/vcfallelicprimitives.1.gz
-man/man1/vcfaltcount.1.gz
-man/man1/vcfannotate.1.gz
-man/man1/vcfannotategenotypes.1.gz
-man/man1/vcfbreakmulti.1.gz
-man/man1/vcfcat.1.gz
-man/man1/vcfcheck.1.gz
-man/man1/vcfclassify.1.gz
-man/man1/vcfcleancomplex.1.gz
-man/man1/vcfcombine.1.gz
-man/man1/vcfcommonsamples.1.gz
-man/man1/vcfcountalleles.1.gz
-man/man1/vcfcreatemulti.1.gz
-man/man1/vcfdistance.1.gz
-man/man1/vcfecho.1.gz
-man/man1/vcfentropy.1.gz
-man/man1/vcfevenregions.1.gz
-man/man1/vcffilter.1.gz
-man/man1/vcffixup.1.gz
-man/man1/vcfflatten.1.gz
-man/man1/vcfgeno2alleles.1.gz
-man/man1/vcfgeno2haplo.1.gz
-man/man1/vcfgenosamplenames.1.gz
-man/man1/vcfgenosummarize.1.gz
-man/man1/vcfgenotypecompare.1.gz
-man/man1/vcfgenotypes.1.gz
-man/man1/vcfglbound.1.gz
-man/man1/vcfglxgt.1.gz
-man/man1/vcfhetcount.1.gz
-man/man1/vcfhethomratio.1.gz
-man/man1/vcfindex.1.gz
-man/man1/vcfinfo2qual.1.gz
-man/man1/vcfinfosummarize.1.gz
-man/man1/vcfintersect.1.gz
-man/man1/vcfkeepgeno.1.gz
-man/man1/vcfkeepinfo.1.gz
-man/man1/vcfkeepsamples.1.gz
-man/man1/vcfld.1.gz
-man/man1/vcfleftalign.1.gz
-man/man1/vcflength.1.gz
-man/man1/vcflib-api.1.gz
-man/man1/vcflib.1.gz
-man/man1/vcfnulldotslashdot.1.gz
-man/man1/vcfnullgenofields.1.gz
-man/man1/vcfnumalt.1.gz
-man/man1/vcfoverlay.1.gz
-man/man1/vcfparsealts.1.gz
-man/man1/vcfprimers.1.gz
-man/man1/vcfqual2info.1.gz
-man/man1/vcfrandom.1.gz
-man/man1/vcfrandomsample.1.gz
-man/man1/vcfremap.1.gz
-man/man1/vcfremoveaberrantgenotypes.1.gz
-man/man1/vcfremovesamples.1.gz
-man/man1/vcfroc.1.gz
-man/man1/vcfsample2info.1.gz
-man/man1/vcfsamplediff.1.gz
-man/man1/vcfsamplenames.1.gz
-man/man1/vcfsitesummarize.1.gz
-man/man1/vcfstats.1.gz
-man/man1/vcfstreamsort.1.gz
-man/man1/vcfuniq.1.gz
-man/man1/vcfuniqalleles.1.gz
-man/man1/vcfwave.1.gz
-man/man1/wcFst.1.gz
+share/man/man1/abba-baba.1.gz
+share/man/man1/bFst.1.gz
+share/man/man1/dumpContigsFromHeader.1.gz
+share/man/man1/genotypeSummary.1.gz
+share/man/man1/hapLrt.1.gz
+share/man/man1/iHS.1.gz
+share/man/man1/meltEHH.1.gz
+share/man/man1/normalize-iHS.1.gz
+share/man/man1/pFst.1.gz
+share/man/man1/pVst.1.gz
+share/man/man1/permuteGPAT++.1.gz
+share/man/man1/permuteSmooth.1.gz
+share/man/man1/plotHaps.1.gz
+share/man/man1/popStats.1.gz
+share/man/man1/pyvcflib.1.gz
+share/man/man1/segmentFst.1.gz
+share/man/man1/segmentIhs.1.gz
+share/man/man1/sequenceDiversity.1.gz
+share/man/man1/smoother.1.gz
+share/man/man1/vcf2dag.1.gz
+share/man/man1/vcf2fasta.1.gz
+share/man/man1/vcf2tsv.1.gz
+share/man/man1/vcfaddinfo.1.gz
+share/man/man1/vcfafpath.1.gz
+share/man/man1/vcfallelicprimitives.1.gz
+share/man/man1/vcfaltcount.1.gz
+share/man/man1/vcfannotate.1.gz
+share/man/man1/vcfannotategenotypes.1.gz
+share/man/man1/vcfbreakmulti.1.gz
+share/man/man1/vcfcat.1.gz
+share/man/man1/vcfcheck.1.gz
+share/man/man1/vcfclassify.1.gz
+share/man/man1/vcfcleancomplex.1.gz
+share/man/man1/vcfcombine.1.gz
+share/man/man1/vcfcommonsamples.1.gz
+share/man/man1/vcfcountalleles.1.gz
+share/man/man1/vcfcreatemulti.1.gz
+share/man/man1/vcfdistance.1.gz
+share/man/man1/vcfecho.1.gz
+share/man/man1/vcfentropy.1.gz
+share/man/man1/vcfevenregions.1.gz
+share/man/man1/vcffilter.1.gz
+share/man/man1/vcffixup.1.gz
+share/man/man1/vcfflatten.1.gz
+share/man/man1/vcfgeno2alleles.1.gz
+share/man/man1/vcfgeno2haplo.1.gz
+share/man/man1/vcfgenosamplenames.1.gz
+share/man/man1/vcfgenosummarize.1.gz
+share/man/man1/vcfgenotypecompare.1.gz
+share/man/man1/vcfgenotypes.1.gz
+share/man/man1/vcfglbound.1.gz
+share/man/man1/vcfglxgt.1.gz
+share/man/man1/vcfhetcount.1.gz
+share/man/man1/vcfhethomratio.1.gz
+share/man/man1/vcfindex.1.gz
+share/man/man1/vcfinfo2qual.1.gz
+share/man/man1/vcfinfosummarize.1.gz
+share/man/man1/vcfintersect.1.gz
+share/man/man1/vcfkeepgeno.1.gz
+share/man/man1/vcfkeepinfo.1.gz
+share/man/man1/vcfkeepsamples.1.gz
+share/man/man1/vcfld.1.gz
+share/man/man1/vcfleftalign.1.gz
+share/man/man1/vcflength.1.gz
+share/man/man1/vcflib-api.1.gz
+share/man/man1/vcflib.1.gz
+share/man/man1/vcfnulldotslashdot.1.gz
+share/man/man1/vcfnullgenofields.1.gz
+share/man/man1/vcfnumalt.1.gz
+share/man/man1/vcfoverlay.1.gz
+share/man/man1/vcfparsealts.1.gz
+share/man/man1/vcfprimers.1.gz
+share/man/man1/vcfqual2info.1.gz
+share/man/man1/vcfrandom.1.gz
+share/man/man1/vcfrandomsample.1.gz
+share/man/man1/vcfremap.1.gz
+share/man/man1/vcfremoveaberrantgenotypes.1.gz
+share/man/man1/vcfremovesamples.1.gz
+share/man/man1/vcfroc.1.gz
+share/man/man1/vcfsample2info.1.gz
+share/man/man1/vcfsamplediff.1.gz
+share/man/man1/vcfsamplenames.1.gz
+share/man/man1/vcfsitesummarize.1.gz
+share/man/man1/vcfstats.1.gz
+share/man/man1/vcfstreamsort.1.gz
+share/man/man1/vcfuniq.1.gz
+share/man/man1/vcfuniqalleles.1.gz
+share/man/man1/vcfwave.1.gz
+share/man/man1/wcFst.1.gz