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Port details
vcflib C++ library and CLI tools for parsing and manipulating VCF files
1.0.2 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.0.0.r1.130_1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-04-17 03:11:48
Last Update: 2021-11-04 14:23:17
Commit Hash: e02229c
License: MIT
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (204 items)
Collapse this list.
  1. /usr/local/share/licenses/vcflib-1.0.2/catalog.mk
  2. /usr/local/share/licenses/vcflib-1.0.2/LICENSE
  3. /usr/local/share/licenses/vcflib-1.0.2/MIT
  4. bin/abba-baba
  5. bin/bFst
  6. bin/dumpContigsFromHeader
  7. bin/genotypeSummary
  8. bin/hapLrt
  9. bin/iHS
  10. bin/meltEHH
  11. bin/normalize-iHS
  12. bin/pFst
  13. bin/pVst
  14. bin/permuteGPAT++
  15. bin/permuteSmooth
  16. bin/plotHaps
  17. bin/popStats
  18. bin/segmentFst
  19. bin/segmentIhs
  20. bin/sequenceDiversity
  21. bin/smoother
  22. bin/vcf2dag
  23. bin/vcf2fasta
  24. bin/vcf2tsv
  25. bin/vcfaddinfo
  26. bin/vcfafpath
  27. bin/vcfallelicprimitives
  28. bin/vcfaltcount
  29. bin/vcfannotate
  30. bin/vcfannotategenotypes
  31. bin/vcfbreakmulti
  32. bin/vcfcat
  33. bin/vcfcheck
  34. bin/vcfclassify
  35. bin/vcfcleancomplex
  36. bin/vcfcombine
  37. bin/vcfcommonsamples
  38. bin/vcfcountalleles
  39. bin/vcfcreatemulti
  40. bin/vcfdistance
  41. bin/vcfecho
  42. bin/vcfentropy
  43. bin/vcfevenregions
  44. bin/vcffilter
  45. bin/vcffixup
  46. bin/vcfflatten
  47. bin/vcfgeno2alleles
  48. bin/vcfgeno2haplo
  49. bin/vcfgenosamplenames
  50. bin/vcfgenosummarize
  51. bin/vcfgenotypecompare
  52. bin/vcfgenotypes
  53. bin/vcfglbound
  54. bin/vcfglxgt
  55. bin/vcfhetcount
  56. bin/vcfhethomratio
  57. bin/vcfindex
  58. bin/vcfinfo2qual
  59. bin/vcfinfosummarize
  60. bin/vcfintersect
  61. bin/vcfkeepgeno
  62. bin/vcfkeepinfo
  63. bin/vcfkeepsamples
  64. bin/vcfld
  65. bin/vcfleftalign
  66. bin/vcflength
  67. bin/vcfnumalt
  68. bin/vcfoverlay
  69. bin/vcfparsealts
  70. bin/vcfprimers
  71. bin/vcfqual2info
  72. bin/vcfrandom
  73. bin/vcfrandomsample
  74. bin/vcfremap
  75. bin/vcfremoveaberrantgenotypes
  76. bin/vcfremovesamples
  77. bin/vcfroc
  78. bin/vcfsample2info
  79. bin/vcfsamplediff
  80. bin/vcfsamplenames
  81. bin/vcfsitesummarize
  82. bin/vcfstats
  83. bin/vcfstreamsort
  84. bin/vcfuniq
  85. bin/vcfuniqalleles
  86. bin/wcFst
  87. include/BandedSmithWaterman.h
  88. include/BedReader.h
  89. include/Fasta.h
  90. include/IndelAllele.h
  91. include/IntervalTree.h
  92. include/LargeFileSupport.h
  93. include/LeftAlign.h
  94. include/Mosaik.h
  95. include/Region.h
  96. include/Repeats.h
  97. include/SmithWatermanGotoh.h
  98. include/Variant.h
  99. include/catch.hpp
  100. include/cdflib.hpp
  101. include/convert.h
  102. include/disorder.h
  103. include/filevercmp.h
  104. include/gpatInfo.hpp
  105. include/join.h
  106. include/mt19937ar.h
  107. include/multichoose.h
  108. include/multipermute.h
  109. include/pdflib.hpp
  110. include/rnglib.hpp
  111. include/split.h
  112. include/ssw.hpp
  113. include/ssw_cpp.hpp
  114. include/var.hpp
  115. include/vec128int.h
  116. include/veclib_types.h
  117. lib/libvcflib.a
  118. man/man1/man/abba-baba.1.gz
  119. man/man1/man/bFst.1.gz
  120. man/man1/man/dumpContigsFromHeader.1.gz
  121. man/man1/man/genotypeSummary.1.gz
  122. man/man1/man/hapLrt.1.gz
  123. man/man1/man/iHS.1.gz
  124. man/man1/man/meltEHH.1.gz
  125. man/man1/man/normalize-iHS.1.gz
  126. man/man1/man/pFst.1.gz
  127. man/man1/man/pVst.1.gz
  128. man/man1/man/permuteGPAT++.1.gz
  129. man/man1/man/permuteSmooth.1.gz
  130. man/man1/man/plotHaps.1.gz
  131. man/man1/man/popStats.1.gz
  132. man/man1/man/segmentFst.1.gz
  133. man/man1/man/segmentIhs.1.gz
  134. man/man1/man/sequenceDiversity.1.gz
  135. man/man1/man/smoother.1.gz
  136. man/man1/man/vcf2dag.1.gz
  137. man/man1/man/vcf2fasta.1.gz
  138. man/man1/man/vcf2tsv.1.gz
  139. man/man1/man/vcfaddinfo.1.gz
  140. man/man1/man/vcfafpath.1.gz
  141. man/man1/man/vcfallelicprimitives.1.gz
  142. man/man1/man/vcfaltcount.1.gz
  143. man/man1/man/vcfannotate.1.gz
  144. man/man1/man/vcfannotategenotypes.1.gz
  145. man/man1/man/vcfbreakmulti.1.gz
  146. man/man1/man/vcfcat.1.gz
  147. man/man1/man/vcfcheck.1.gz
  148. man/man1/man/vcfclassify.1.gz
  149. man/man1/man/vcfcleancomplex.1.gz
  150. man/man1/man/vcfcombine.1.gz
  151. man/man1/man/vcfcommonsamples.1.gz
  152. man/man1/man/vcfcountalleles.1.gz
  153. man/man1/man/vcfcreatemulti.1.gz
  154. man/man1/man/vcfdistance.1.gz
  155. man/man1/man/vcfecho.1.gz
  156. man/man1/man/vcfentropy.1.gz
  157. man/man1/man/vcfevenregions.1.gz
  158. man/man1/man/vcffilter.1.gz
  159. man/man1/man/vcffixup.1.gz
  160. man/man1/man/vcfflatten.1.gz
  161. man/man1/man/vcfgeno2alleles.1.gz
  162. man/man1/man/vcfgeno2haplo.1.gz
  163. man/man1/man/vcfgenosamplenames.1.gz
  164. man/man1/man/vcfgenosummarize.1.gz
  165. man/man1/man/vcfgenotypecompare.1.gz
  166. man/man1/man/vcfgenotypes.1.gz
  167. man/man1/man/vcfglbound.1.gz
  168. man/man1/man/vcfglxgt.1.gz
  169. man/man1/man/vcfhetcount.1.gz
  170. man/man1/man/vcfhethomratio.1.gz
  171. man/man1/man/vcfindex.1.gz
  172. man/man1/man/vcfinfo2qual.1.gz
  173. man/man1/man/vcfinfosummarize.1.gz
  174. man/man1/man/vcfintersect.1.gz
  175. man/man1/man/vcfkeepgeno.1.gz
  176. man/man1/man/vcfkeepinfo.1.gz
  177. man/man1/man/vcfkeepsamples.1.gz
  178. man/man1/man/vcfld.1.gz
  179. man/man1/man/vcfleftalign.1.gz
  180. man/man1/man/vcflength.1.gz
  181. man/man1/man/vcflib.1.gz
  182. man/man1/man/vcfnumalt.1.gz
  183. man/man1/man/vcfoverlay.1.gz
  184. man/man1/man/vcfparsealts.1.gz
  185. man/man1/man/vcfprimers.1.gz
  186. man/man1/man/vcfqual2info.1.gz
  187. man/man1/man/vcfrandom.1.gz
  188. man/man1/man/vcfrandomsample.1.gz
  189. man/man1/man/vcfremap.1.gz
  190. man/man1/man/vcfremoveaberrantgenotypes.1.gz
  191. man/man1/man/vcfremovesamples.1.gz
  192. man/man1/man/vcfroc.1.gz
  193. man/man1/man/vcfsample2info.1.gz
  194. man/man1/man/vcfsamplediff.1.gz
  195. man/man1/man/vcfsamplenames.1.gz
  196. man/man1/man/vcfsitesummarize.1.gz
  197. man/man1/man/vcfstats.1.gz
  198. man/man1/man/vcfstreamsort.1.gz
  199. man/man1/man/vcfuniq.1.gz
  200. man/man1/man/vcfuniqalleles.1.gz
  201. man/man1/man/wcFst.1.gz
  202. @owner
  203. @group
  204. @mode
Collapse this list.
Dependency lines:
  • vcflib>0:biology/vcflib
To install the port:
cd /usr/ports/biology/vcflib/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/vcflib
  • pkg install vcflib
PKGNAME: vcflib
Flavors: there is no flavor information for this port.
distinfo:
Packages (timestamps in pop-ups are UTC):
vcflib
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd641.0.0.r1.130_11.0.0.r1.130_1
FreeBSD:11:armv6--
FreeBSD:11:i3861.0.0.r1.130_11.0.0.r1.130_1
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64--
FreeBSD:12:amd641.0.21.0.0.r1.130_1
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i3861.0.21.0.0.r1.130_1
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd641.0.21.0.0.r1.130_1
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i3861.0.21.0.0.r1.130_1
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch641.0.2-
FreeBSD:14:amd641.0.2-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i3861.0.2-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. cmake : devel/cmake
  2. ninja : devel/ninja
  3. pkgconf>=1.3.0_1 : devel/pkgconf
Library dependencies:
  1. libhts.so : biology/htslib
  2. libtabix.so : biology/tabixpp
This port is required by:
for Run
  1. biology/ddocent

Configuration Options:
Options name:

USES:

FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/ekg/vcflib/tar.gz/v1.0.2?dummy=/
Collapse this list.

Number of commits found: 8

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
04 Nov 2021 14:23:17
 files touched by this commit commit hash:e02229c22ccbe188c405dcb5d81d14e5c809411e  1.0.2
Jason W. Bacon (jwb) search for other commits by this committer
biology/vcflib: Update to 1.0.2

Switch to github submodules for most deps rather than patch build system
Fixes build on powerpc64 and aarch64, possibly others

Changes:        https://github.com/vcflib/vcflib/tags

PR:             259622
Reported by:    pkubaj
07 Apr 2021 08:09:01
 files touched by this commit commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  1.0.0.r1.130_1
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  1.0.0.r1.130_1
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
28 Mar 2021 16:39:24
Original commit files touched by this commit Revision:569399  1.0.0.r1.130_1
pkubaj search for other commits by this committer
biology/vcflib: fix build on powerpc64le

Use GCC for its SSE -> AltiVec translation:
In file included from src/ssw.cpp:38:
In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13:
/usr/lib/clang/11.0.1/include/mmintrin.h:33:5: error: use of undeclared
identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'?
    __builtin_ia32_emms();
02 Jan 2021 01:46:09
Original commit files touched by this commit Revision:559904  1.0.0.r1.130_1
linimon search for other commits by this committer
For ports on riscv64 that fail the same (or similar ways) to aarch64, mark
them BROKEN.

While here, pet portlint (Makevar order).

Approved by:	portmgr (tier-2 blanket)
03 Aug 2020 17:40:04
Original commit files touched by this commit Revision:544090  1.0.0.r1.130_1
jwb search for other commits by this committer
biology/htslib: Upgrade to 1.10.2

Numerous bug fixes and enhancements since 1.9:
https://github.com/samtools/htslib/tags

Bump PORTREVISION on dependents that don't require additional patching

PR:             248089
22 Jun 2018 00:03:08
Original commit files touched by this commit Revision:473010  1.0.0.r1.130
linimon search for other commits by this committer
Mark these ports as broken on aarch64.

Approved by:	portmgr (tier-2 blanket)
17 Apr 2018 03:11:39
Original commit files touched by this commit Revision:467553  1.0.0.r1.130
jwb search for other commits by this committer
biology/vcflib: C++ library and CLI tools for parsing and manipulating VCF files

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15109

Number of commits found: 8