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Port details on branch 2022Q2
vcflib C++ library and CLI tools for parsing and manipulating VCF files
1.0.10 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 1.0.7_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: 2024-04-22 12:42:04
Commit Hash: 86c8816
License: MIT
WWW:
https://github.com/vcflib/vcflib
Description:
The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended to concisely describe reference-indexed variations between individuals. VCF provides a common interchange format for the description of variation in individuals and populations of samples, and has become the defacto standard reporting format for a wide array of genomic variant detectors. vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. It is both: an API for parsing and operating on records of genomic variation as it can be described by the VCF format and a collection of command-line utilities for executing complex manipulations on VCF files. The API itself provides a quick and extremely permissive method to read and write VCF files. Extensions and applications of the library provided in the included utilities (*.cpp) comprise the vast bulk of the library's utility for most users.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (255 items)
Collapse this list.
  1. /usr/local/share/licenses/vcflib-1.0.10/catalog.mk
  2. /usr/local/share/licenses/vcflib-1.0.10/LICENSE
  3. /usr/local/share/licenses/vcflib-1.0.10/MIT
  4. bin/abba-baba
  5. bin/bFst
  6. bin/bed2region
  7. bin/bgziptabix
  8. bin/dumpContigsFromHeader
  9. bin/genotypeSummary
  10. bin/hapLrt
  11. bin/iHS
  12. bin/meltEHH
  13. bin/normalize-iHS
  14. bin/pFst
  15. bin/pVst
  16. bin/permuteGPAT++
  17. bin/permuteSmooth
  18. bin/plotHaps
  19. bin/popStats
  20. bin/segmentFst
  21. bin/segmentIhs
  22. bin/sequenceDiversity
  23. bin/smoother
  24. bin/vcf2bed.py
  25. bin/vcf2dag
  26. bin/vcf2fasta
  27. bin/vcf2sqlite.py
  28. bin/vcf2tsv
  29. bin/vcf_strip_extra_headers
  30. bin/vcfaddinfo
  31. bin/vcfafpath
  32. bin/vcfallelicprimitives
  33. bin/vcfaltcount
  34. bin/vcfannotate
  35. bin/vcfannotategenotypes
  36. bin/vcfbiallelic
  37. bin/vcfbreakmulti
  38. bin/vcfcat
  39. bin/vcfcheck
  40. bin/vcfclassify
  41. bin/vcfcleancomplex
  42. bin/vcfclearid
  43. bin/vcfclearinfo
  44. bin/vcfcombine
  45. bin/vcfcommonsamples
  46. bin/vcfcomplex
  47. bin/vcfcountalleles
  48. bin/vcfcreatemulti
  49. bin/vcfdistance
  50. bin/vcfecho
  51. bin/vcfentropy
  52. bin/vcfevenregions
  53. bin/vcffilter
  54. bin/vcffirstheader
  55. bin/vcffixup
  56. bin/vcfflatten
  57. bin/vcfgeno2alleles
  58. bin/vcfgeno2haplo
  59. bin/vcfgenosamplenames
  60. bin/vcfgenosummarize
  61. bin/vcfgenotypecompare
  62. bin/vcfgenotypes
  63. bin/vcfglbound
  64. bin/vcfglxgt
  65. bin/vcfgtcompare.sh
  66. bin/vcfhetcount
  67. bin/vcfhethomratio
  68. bin/vcfindelproximity
  69. bin/vcfindels
  70. bin/vcfindex
  71. bin/vcfinfo2qual
  72. bin/vcfinfosummarize
  73. bin/vcfintersect
  74. bin/vcfjoincalls
  75. bin/vcfkeepgeno
  76. bin/vcfkeepinfo
  77. bin/vcfkeepsamples
  78. bin/vcfld
  79. bin/vcfleftalign
  80. bin/vcflength
  81. bin/vcfmultiallelic
  82. bin/vcfmultiway
  83. bin/vcfmultiwayscripts
  84. bin/vcfnobiallelicsnps
  85. bin/vcfnoindels
  86. bin/vcfnosnps
  87. bin/vcfnulldotslashdot
  88. bin/vcfnullgenofields
  89. bin/vcfnumalt
  90. bin/vcfoverlay
  91. bin/vcfparsealts
  92. bin/vcfplotaltdiscrepancy.r
  93. bin/vcfplotaltdiscrepancy.sh
  94. bin/vcfplotsitediscrepancy.r
  95. bin/vcfplottstv.sh
  96. bin/vcfprimers
  97. bin/vcfprintaltdiscrepancy.r
  98. bin/vcfprintaltdiscrepancy.sh
  99. bin/vcfqual2info
  100. bin/vcfqualfilter
  101. bin/vcfrandom
  102. bin/vcfrandomsample
  103. bin/vcfregionreduce
  104. bin/vcfregionreduce_and_cut
  105. bin/vcfregionreduce_pipe
  106. bin/vcfregionreduce_uncompressed
  107. bin/vcfremap
  108. bin/vcfremoveaberrantgenotypes
  109. bin/vcfremovenonATGC
  110. bin/vcfremovesamples
  111. bin/vcfroc
  112. bin/vcfsample2info
  113. bin/vcfsamplediff
  114. bin/vcfsamplenames
  115. bin/vcfsitesummarize
  116. bin/vcfsnps
  117. bin/vcfsort
  118. bin/vcfstats
  119. bin/vcfstreamsort
  120. bin/vcfuniq
  121. bin/vcfuniqalleles
  122. bin/vcfvarstats
  123. bin/vcfwave
  124. bin/wcFst
  125. include/BandedSmithWaterman.h
  126. include/BedReader.h
  127. include/Fasta.h
  128. include/IndelAllele.h
  129. include/IntervalTree.h
  130. include/LargeFileSupport.h
  131. include/LeftAlign.h
  132. include/LeftAlign.hpp
  133. include/Mosaik.h
  134. include/Region.h
  135. include/Repeats.h
  136. include/SmithWatermanGotoh.h
  137. include/Variant.h
  138. include/allele.hpp
  139. include/catch.hpp
  140. include/cdflib.hpp
  141. include/cigar.hpp
  142. include/convert.h
  143. include/disorder.h
  144. include/filevercmp.h
  145. include/gpatInfo.hpp
  146. include/join.h
  147. include/makeUnique.h
  148. include/mt19937ar.h
  149. include/multichoose.h
  150. include/multipermute.h
  151. include/murmur3.hpp
  152. include/pdflib.hpp
  153. include/rkmh.hpp
  154. include/rnglib.hpp
  155. include/split.h
  156. include/ssw.hpp
  157. include/ssw_cpp.hpp
  158. include/var.hpp
  159. include/vcf-c-api.h
  160. include/vcf-wfa.h
  161. lib/libvcflib.a
  162. @comment lib/libzig.a
  163. lib/pyvcflib.cpython-39.so
  164. share/man/man1/abba-baba.1.gz
  165. share/man/man1/bFst.1.gz
  166. share/man/man1/dumpContigsFromHeader.1.gz
  167. share/man/man1/genotypeSummary.1.gz
  168. share/man/man1/hapLrt.1.gz
  169. share/man/man1/iHS.1.gz
  170. share/man/man1/meltEHH.1.gz
  171. share/man/man1/normalize-iHS.1.gz
  172. share/man/man1/pFst.1.gz
  173. share/man/man1/pVst.1.gz
  174. share/man/man1/permuteGPAT++.1.gz
  175. share/man/man1/permuteSmooth.1.gz
  176. share/man/man1/plotHaps.1.gz
  177. share/man/man1/popStats.1.gz
  178. share/man/man1/pyvcflib.1.gz
  179. share/man/man1/segmentFst.1.gz
  180. share/man/man1/segmentIhs.1.gz
  181. share/man/man1/sequenceDiversity.1.gz
  182. share/man/man1/smoother.1.gz
  183. share/man/man1/vcf2dag.1.gz
  184. share/man/man1/vcf2fasta.1.gz
  185. share/man/man1/vcf2tsv.1.gz
  186. share/man/man1/vcfaddinfo.1.gz
  187. share/man/man1/vcfafpath.1.gz
  188. share/man/man1/vcfallelicprimitives.1.gz
  189. share/man/man1/vcfaltcount.1.gz
  190. share/man/man1/vcfannotate.1.gz
  191. share/man/man1/vcfannotategenotypes.1.gz
  192. share/man/man1/vcfbreakmulti.1.gz
  193. share/man/man1/vcfcat.1.gz
  194. share/man/man1/vcfcheck.1.gz
  195. share/man/man1/vcfclassify.1.gz
  196. share/man/man1/vcfcleancomplex.1.gz
  197. share/man/man1/vcfcombine.1.gz
  198. share/man/man1/vcfcommonsamples.1.gz
  199. share/man/man1/vcfcountalleles.1.gz
  200. share/man/man1/vcfcreatemulti.1.gz
  201. share/man/man1/vcfdistance.1.gz
  202. share/man/man1/vcfecho.1.gz
  203. share/man/man1/vcfentropy.1.gz
  204. share/man/man1/vcfevenregions.1.gz
  205. share/man/man1/vcffilter.1.gz
  206. share/man/man1/vcffixup.1.gz
  207. share/man/man1/vcfflatten.1.gz
  208. share/man/man1/vcfgeno2alleles.1.gz
  209. share/man/man1/vcfgeno2haplo.1.gz
  210. share/man/man1/vcfgenosamplenames.1.gz
  211. share/man/man1/vcfgenosummarize.1.gz
  212. share/man/man1/vcfgenotypecompare.1.gz
  213. share/man/man1/vcfgenotypes.1.gz
  214. share/man/man1/vcfglbound.1.gz
  215. share/man/man1/vcfglxgt.1.gz
  216. share/man/man1/vcfhetcount.1.gz
  217. share/man/man1/vcfhethomratio.1.gz
  218. share/man/man1/vcfindex.1.gz
  219. share/man/man1/vcfinfo2qual.1.gz
  220. share/man/man1/vcfinfosummarize.1.gz
  221. share/man/man1/vcfintersect.1.gz
  222. share/man/man1/vcfkeepgeno.1.gz
  223. share/man/man1/vcfkeepinfo.1.gz
  224. share/man/man1/vcfkeepsamples.1.gz
  225. share/man/man1/vcfld.1.gz
  226. share/man/man1/vcfleftalign.1.gz
  227. share/man/man1/vcflength.1.gz
  228. share/man/man1/vcflib-api.1.gz
  229. share/man/man1/vcflib.1.gz
  230. share/man/man1/vcfnulldotslashdot.1.gz
  231. share/man/man1/vcfnullgenofields.1.gz
  232. share/man/man1/vcfnumalt.1.gz
  233. share/man/man1/vcfoverlay.1.gz
  234. share/man/man1/vcfparsealts.1.gz
  235. share/man/man1/vcfprimers.1.gz
  236. share/man/man1/vcfqual2info.1.gz
  237. share/man/man1/vcfrandom.1.gz
  238. share/man/man1/vcfrandomsample.1.gz
  239. share/man/man1/vcfremap.1.gz
  240. share/man/man1/vcfremoveaberrantgenotypes.1.gz
  241. share/man/man1/vcfremovesamples.1.gz
  242. share/man/man1/vcfroc.1.gz
  243. share/man/man1/vcfsample2info.1.gz
  244. share/man/man1/vcfsamplediff.1.gz
  245. share/man/man1/vcfsamplenames.1.gz
  246. share/man/man1/vcfsitesummarize.1.gz
  247. share/man/man1/vcfstats.1.gz
  248. share/man/man1/vcfstreamsort.1.gz
  249. share/man/man1/vcfuniq.1.gz
  250. share/man/man1/vcfuniqalleles.1.gz
  251. share/man/man1/vcfwave.1.gz
  252. share/man/man1/wcFst.1.gz
  253. @owner
  254. @group
  255. @mode
Collapse this list.
Dependency lines:
  • vcflib>0:biology/vcflib
Conflicts:
CONFLICTS_INSTALL:
  • filevercmp
  • libdisorder
Conflicts Matches:
There are no Conflicts Matches for this port. This is usually an error.
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
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: vcflib
Flavors: there is no flavor information for this port.
NOT_FOR_ARCHS: armv6 armv7
distinfo:
TIMESTAMP = 1713703391 SHA256 (ekg-vcflib-v1.0.10_GH0.tar.gz) = 6f7f366555e5b191a509bda6d7a2078825827458ba7e9922094c4c1ebb48e693 SIZE (ekg-vcflib-v1.0.10_GH0.tar.gz) = 23539349

Expand this list (18 items)

Collapse this list.

SHA256 (ekg-fastahack-bb33265_GH0.tar.gz) = f671609e1a8d7cacb00065bf307c90c46116af8e5cea939b06edcdbcc6d4bc2a SIZE (ekg-fastahack-bb33265_GH0.tar.gz) = 18760 SHA256 (ekg-filevercmp-df20dcc_GH0.tar.gz) = d34bec614be638e05eb6fa419c936b9e7de58d50b1a096a5ca02aadb7db6b059 SIZE (ekg-filevercmp-df20dcc_GH0.tar.gz) = 3113 SHA256 (ekg-fsom-56695e1_GH0.tar.gz) = d1cc62bf72a75b74149336799fcbe237eaa662161fb0cfdac5ba6d5825248180 SIZE (ekg-fsom-56695e1_GH0.tar.gz) = 9767 SHA256 (ekg-intervaltree-aa59377_GH0.tar.gz) = 8d42eee645bcb196da03077c6f567f61529add3a581bb98d85f5c9cfe4b50774 SIZE (ekg-intervaltree-aa59377_GH0.tar.gz) = 72545 SHA256 (edawson-libVCFH-44b6580_GH0.tar.gz) = 3c90a6c5f1fbe88bedb4a0dcdc1e55dfa51c58f2acd9b31bceead226ab84785c SIZE (edawson-libVCFH-44b6580_GH0.tar.gz) = 2956 SHA256 (ekg-multichoose-e1f94ae_GH0.tar.gz) = 78ffaa36b6f82685230a3d263c9b556ab55a97196036764473f2b1ee66997ca8 SIZE (ekg-multichoose-e1f94ae_GH0.tar.gz) = 6585 SHA256 (ekg-smithwaterman-2610e25_GH0.tar.gz) = f907becb50945d0858d3bf7a64959905712244cbe8455b35ef1102ff893173ce SIZE (ekg-smithwaterman-2610e25_GH0.tar.gz) = 39160 SHA256 (simd-everywhere-simde-no-tests-9af03cd_GH0.tar.gz) = 99dcb7d6a2e1dc3f51401ff16eaa5dde93c793e13b514ea9cae4d9819144b8fe SIZE (simd-everywhere-simde-no-tests-9af03cd_GH0.tar.gz) = 572867 SHA256 (vcflib-tabixpp-v1.1.2_GH0.tar.gz) = c850299c3c495221818a85c9205c60185c8ed9468d5ec2ed034470bb852229dc SIZE (vcflib-tabixpp-v1.1.2_GH0.tar.gz) = 6962

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Packages (timestamps in pop-ups are UTC):
vcflib
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest1.0.101.0.10--1.0.10---
FreeBSD:13:quarterly1.0.7_11.0.7_1--1.0.7_1-1.0.71.0.7
FreeBSD:14:latest1.0.7_11.0.101.0.3_1-1.0.10--1.0.7
FreeBSD:14:quarterly1.0.7_11.0.7_1--1.0.7_1-1.0.71.0.7
FreeBSD:15:latest1.0.101.0.10n/a-n/a-1.0.71.0.7
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. pybind11>0 : devel/pybind11
  2. cmake : devel/cmake-core
  3. gmake>=4.4.1 : devel/gmake
  4. pkgconf>=1.3.0_1 : devel/pkgconf
  5. python3.9 : lang/python39
Test dependencies:
  1. python3.9 : lang/python39
Runtime dependencies:
  1. python3.9 : lang/python39
Library dependencies:
  1. libhts.so : biology/htslib
  2. libcurl.so : ftp/curl
  3. libwfa2.so : biology/wfa2-lib
This port is required by:
for Run
  1. biology/ddocent
Configuration Options:
===> The following configuration options are available for vcflib-1.0.10: ZIG=off: Include Zig language support ===> Use 'make config' to modify these settings
Options name:
biology_vcflib
USES:
cmake:noninja gmake localbase:ldflags pkgconfig python shebangfix
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/v1.0.10?dummy=/
Collapse this list.

There are no commits on branch 2022Q2 for this port
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