broadinstitute/barclay

Issues

• Required collection arguments do not allow resetting the collection using null

  #201 opened a month ago by kshakir
  0

• Confusing error messages when `@BetaFeature` and `@ExperimentalFeature` both used on the same Class.

  #200 opened 8 months ago by jonn-smith
  1

• Feature request: render Javadoc value tag correctly.

  #189 opened 2 years ago by samuelklee
  2

• [Debian] Switching to OpenJDK 17: issues

  #185 opened 3 years ago by pgrt
  3

• [Debian] four flaky tests in version 4.0.1

  #184 opened 3 years ago by pgrt
  2

• Repeated "Possible Values{" in help output.

  #182 opened 3 years ago by lbergelson
  0

• Feature Request: parse shell quotes in an arguments file

  #181 opened 3 years ago by GATKSupportTeam
  4

• Question about iterating LinkedHashMap in Freemarker

  #168 opened 4 years ago by pgrt
  2

• Barlcay parser doesn't include positional args in the usage string

  #173 opened 4 years ago by cmnbroad
  0

• Tab completion treats all DocumentedFeatures as completion targets

  #109 opened 5 years ago by cmnbroad
  0

• Option prefix should not be included in the freemarker map

  #163 opened 5 years ago by cmnbroad
  0

• Late failure on a argument collection field with no initialization value (therefore null) v

  #155 opened 5 years ago by vruano
  1

• Add a way to define an "argset" as a named collection of default argument values

  #154 opened 5 years ago by cmnbroad
  0

• Make arguments_file expansion Path aware

  #153 opened 6 years ago by cmnbroad
  0

• Java 9 deprecation

  #137 opened 7 years ago by osallou
  7

• CommandLineParser tests should only test one feature per test case

  #150 opened 6 years ago by cmnbroad
  0

• Plugin doc integration

  #148 opened 6 years ago by cmnbroad
  0

• Collection of enums annotated with Argument are not showing possible values

  #142 opened 6 years ago by magicDGS
  2

• CommandLinePluginDescriptor.includePluginClass() flipped?

  #131 opened 6 years ago by bbimber
  1

• Barclay CLP should reject hybrid posix syntax (-I=somevalue)

  #145 opened 6 years ago by cmnbroad
  0

• Allow @Argument annotations to declare valid option values

  #144 opened 6 years ago by cmnbroad
  0

• Mutexes don't null out default arguments

  #143 opened 6 years ago by helgridly
  2

• Ability to have "shoort or long options" passed as args to jopt parser

  #140 opened 7 years ago by smutalik
  3

• ArgumentDefinition.toCommandLineString for enums uses toString instead of name

  #139 opened 7 years ago by magicDGS
  0

• Plugin descriptors with several instances with different arguments

  #138 opened 7 years ago by magicDGS
  4

• Consider disabling jopt short option clustering in Barclay Parser

  #119 opened 7 years ago by cmnbroad
  5

• Define a public API for CommandLineArgumentParser and CommandLineProgram

  #127 opened 7 years ago by cmnbroad
  2

• Proposal: use java bean validation (JSR 380) for constraint arguments

  #134 opened 7 years ago by magicDGS
  2

• Host Barclay javadoc on Github Pages.

  #132 opened 7 years ago by cmnbroad
  0

• Add a CustomCommandLineArgument interface

  #130 opened 7 years ago by cmnbroad
  5

• Tag 2.0.0 tag does not appear in releases

  #129 opened 7 years ago by magicDGS
  1

• Add @DocumentedFeature support for classes that have no @Argument fields

  #128 opened 7 years ago by cmnbroad
  0

• some HTML tags do not get stripped from arguments.

  #124 opened 7 years ago by yfarjoun
  0

• CommandLineArgumentParser help output doesn't include plugin values

  #121 opened 7 years ago by cmnbroad
  0

• SpecialArgumentsCollection has outdated argument names

  #120 opened 7 years ago by jamesemery
  2

• WordWrap the preamble, not only the argument description.

  #103 opened 7 years ago by yfarjoun
  0

• Legacy parser doesn't enforce required collections to be provided.

  #117 opened 7 years ago by cmnbroad
  0

• Barclay parser doesn't render embedded html as text in usage output

  #112 opened 7 years ago by cmnbroad
  4

• Barclay could throw a more helpful error message when trying to populate an immutable list argument field.

  #100 opened 7 years ago by jamesemery
  6

• Check that types with optional @Arguments are nullable

  #115 opened 7 years ago by yfarjoun
  1

• fix ClassFinder bug with directories that include the + character

  #113 opened 7 years ago by lbergelson
  0

• Change the list file argument expansion extension from ".list" to ".args"

  #94 opened 7 years ago by cmnbroad
  0

• Field level javadoc can be incorrect

  #104 opened 7 years ago by cmnbroad
  1

• DocumentedFeatures do not populate arguments

  #97 opened 7 years ago by magicDGS
  2

• Add support for java.io.Path

  #106 opened 7 years ago by pshapiro4broad
  9

• Need a mock Doclet/RootDoc/ClassDoc/FieldDoc tree for unit testing

  #107 opened 7 years ago by cmnbroad
  0

• Error of not setting required primitive-typed argument not being caught

  #101 opened 7 years ago by SHuang-Broad
  4

• Provide annotation for tools to be "@Hidden"

  #92 opened 7 years ago by SHuang-Broad
  12

• Embedded tags cause some javadoc to be dropped from the docgen output

  #87 opened 7 years ago by cmnbroad
  0

• Discussion: how to deal with javadoc-link tags

  #85 opened 7 years ago by magicDGS
  2