Ecosyste.ms: Issues

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GitHub / acorg/light-matter issues and pull requests

#100 - Added version numbers to requirements.txt

Pull Request - State: closed - Opened by terrycojones about 10 years ago - 1 comment

#100 - Added version numbers to requirements.txt

Pull Request - State: closed - Opened by terrycojones about 10 years ago - 1 comment

#99 - Add version numbers to requirements.txt

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#99 - Add version numbers to requirements.txt

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#98 - Added checksum checking in LightReadsAlignments

Pull Request - State: closed - Opened by bamueh about 10 years ago - 6 comments

#97 - Added default landmark and trig point finder classes for db creation

Pull Request - State: closed - Opened by terrycojones about 10 years ago - 3 comments

#97 - Added default landmark and trig point finder classes for db creation

Pull Request - State: closed - Opened by terrycojones about 10 years ago - 3 comments

#96 - Save database to JSON

Pull Request - State: closed - Opened by terrycojones about 10 years ago - 1 comment

#96 - Save database to JSON

Pull Request - State: closed - Opened by terrycojones about 10 years ago - 1 comment

#95 - The LightReadsAlignments class should check result and database checksums

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#95 - The LightReadsAlignments class should check result and database checksums

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#94 - Save database to JSON format

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#94 - Save database to JSON format

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#93 - Add a database-details.py script

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#93 - Add a database-details.py script

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#92 - Add a default set of landmark and trig point finders to be used when building databases

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#92 - Add a default set of landmark and trig point finders to be used when building databases

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#91 - Add dark matter result reader

Pull Request - State: closed - Opened by terrycojones about 10 years ago

#90 - Fixed docstrings in test_amino_acids.py

Pull Request - State: closed - Opened by bamueh about 10 years ago - 2 comments

#90 - Fixed docstrings in test_amino_acids.py

Pull Request - State: closed - Opened by bamueh about 10 years ago - 2 comments

#89 - The docstrings on the tests in test_amino_acids.py are all identical

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: bug

#89 - The docstrings on the tests in test_amino_acids.py are all identical

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: bug

#88 - Added additional information to hsp

Pull Request - State: closed - Opened by bamueh about 10 years ago - 2 comments

#88 - Added additional information to hsp

Pull Request - State: closed - Opened by bamueh about 10 years ago - 2 comments

#87 - Added aboveMeanThreshold to database.find function.

Pull Request - State: closed - Opened by terrycojones about 10 years ago - 1 comment

#87 - Added aboveMeanThreshold to database.find function.

Pull Request - State: closed - Opened by terrycojones about 10 years ago - 1 comment

#86 - Simplify tests in test_result

Issue - State: closed - Opened by terrycojones about 10 years ago - 2 comments
Labels: enhancement

#86 - Simplify tests in test_result

Issue - State: closed - Opened by terrycojones about 10 years ago - 2 comments
Labels: enhancement

#85 - Parameterize database.find to add an aboveMeanThreshold argument

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#85 - Parameterize database.find to add an aboveMeanThreshold argument

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#84 - Add more information to result HSPs

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#84 - Add more information to result HSPs

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#83 - Add integration with dark titles alignments

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#83 - Add integration with dark titles alignments

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#82 - Added checksum to database

Pull Request - State: closed - Opened by terrycojones about 10 years ago - 1 comment

#82 - Added checksum to database

Pull Request - State: closed - Opened by terrycojones about 10 years ago - 1 comment

#81 - Fixed failing tests for testSave

Pull Request - State: closed - Opened by bamueh about 10 years ago

#80 - SubjectInfo now contains subject.id and subject.sequence

Pull Request - State: closed - Opened by bamueh about 10 years ago

#80 - SubjectInfo now contains subject.id and subject.sequence

Pull Request - State: closed - Opened by bamueh about 10 years ago

#79 - Change language of databases to use 'subject' not 'read'

Pull Request - State: closed - Opened by terrycojones about 10 years ago

#79 - Change language of databases to use 'subject' not 'read'

Pull Request - State: closed - Opened by terrycojones about 10 years ago

#78 - Added read sequence to Result

Pull Request - State: closed - Opened by bamueh about 10 years ago

#78 - Added read sequence to Result

Pull Request - State: closed - Opened by bamueh about 10 years ago

#76 - Add read sequences to the results output format

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#76 - Add read sequences to the results output format

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#75 - Change the language in the database code to talk about subjects

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#75 - Change the language in the database code to talk about subjects

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#74 - Add sequences to the database

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#74 - Add sequences to the database

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#73 - Added subjectTitle to saved JSON result.

Pull Request - State: closed - Opened by terrycojones about 10 years ago - 1 comment

#73 - Added subjectTitle to saved JSON result.

Pull Request - State: closed - Opened by terrycojones about 10 years ago - 1 comment

#72 - Add a 'subjectTitle' key to saved result JSON output

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#72 - Add a 'subjectTitle' key to saved result JSON output

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#71 - Added function to plot all landmark and trigpoint pairs on a read

Pull Request - State: closed - Opened by bamueh about 10 years ago

#71 - Added function to plot all landmark and trigpoint pairs on a read

Pull Request - State: closed - Opened by bamueh about 10 years ago

#70 - Test...

Issue - State: closed - Opened by terrycojones about 10 years ago - 1 comment

#70 - Test...

Issue - State: closed - Opened by terrycojones about 10 years ago - 1 comment

#69 - Added list-finders.py and list-symbols.py

Pull Request - State: closed - Opened by terrycojones about 10 years ago - 5 comments

#69 - Added list-finders.py and list-symbols.py

Pull Request - State: closed - Opened by terrycojones about 10 years ago - 5 comments

#68 - Add script to print all landmark and trig point finder symbols

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#67 - Changed default aa in amino_acids.py

Pull Request - State: closed - Opened by bamueh about 10 years ago

#66 - Added simple beta strand finder and tests.

Pull Request - State: closed - Opened by terrycojones about 10 years ago

#66 - Added simple beta strand finder and tests.

Pull Request - State: closed - Opened by terrycojones about 10 years ago

#65 - Remove use of mutable default argument in amino_acid.py

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: bug

#65 - Remove use of mutable default argument in amino_acid.py

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: bug

#64 - Added trig point finder based on peaks of one property in a sequence window.

Pull Request - State: open - Opened by bamueh about 10 years ago - 1 comment

#63 - Added trig point finders based on individual amino acid property peaks

Pull Request - State: closed - Opened by bamueh about 10 years ago

#63 - Added trig point finders based on individual amino acid property peaks

Pull Request - State: closed - Opened by bamueh about 10 years ago

#61 - Performance test suite

Pull Request - State: closed - Opened by bamueh about 10 years ago

#60 - Fixed coverage bug

Pull Request - State: closed - Opened by bamueh about 10 years ago - 1 comment

#60 - Fixed coverage bug

Pull Request - State: closed - Opened by bamueh about 10 years ago - 1 comment

#59 - Changes to significancy testing

Pull Request - State: closed - Opened by bamueh about 10 years ago

#59 - Changes to significancy testing

Pull Request - State: closed - Opened by bamueh about 10 years ago

#58 - Divide by zero error in test suite

Issue - State: closed - Opened by terrycojones about 10 years ago - 1 comment
Labels: bug

#58 - Divide by zero error in test suite

Issue - State: closed - Opened by terrycojones about 10 years ago - 1 comment
Labels: bug

#57 - Fix problem with hash or coverage count in create-database.py

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: bug

#57 - Fix problem with hash or coverage count in create-database.py

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: bug

#56 - Added file to run tests

Pull Request - State: closed - Opened by bamueh about 10 years ago

#56 - Added file to run tests

Pull Request - State: closed - Opened by bamueh about 10 years ago

#55 - Add a bin script for testing.

Issue - State: closed - Opened by bamueh about 10 years ago

#55 - Add a bin script for testing.

Issue - State: closed - Opened by bamueh about 10 years ago

#53 - Make a performance test suite

Issue - State: closed - Opened by bamueh about 10 years ago

#53 - Make a performance test suite

Issue - State: closed - Opened by bamueh about 10 years ago

#52 - Write a beta strand landmark finder

Issue - State: closed - Opened by bamueh about 10 years ago
Labels: enhancement

#52 - Write a beta strand landmark finder

Issue - State: closed - Opened by bamueh about 10 years ago
Labels: enhancement

#51 - Write ScannedReadDatabaseResult.significant to JSON instead of ScannedReadDatabaseResult.matches

Issue - State: closed - Opened by bamueh about 10 years ago - 2 comments
Labels: question

#51 - Write ScannedReadDatabaseResult.significant to JSON instead of ScannedReadDatabaseResult.matches

Issue - State: closed - Opened by bamueh about 10 years ago - 2 comments
Labels: question

#50 - ScannedReadDatabaseResult.save should write one line of JSON

Pull Request - State: closed - Opened by bamueh about 10 years ago - 1 comment

#50 - ScannedReadDatabaseResult.save should write one line of JSON

Pull Request - State: closed - Opened by bamueh about 10 years ago - 1 comment

#49 - Save read (subject) indices in the database

Pull Request - State: closed - Opened by terrycojones about 10 years ago

#49 - Save read (subject) indices in the database

Pull Request - State: closed - Opened by terrycojones about 10 years ago

#48 - Database file should include titles and lengths at start

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#48 - Database file should include titles and lengths at start

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#47 - Write database params to a file

Pull Request - State: closed - Opened by terrycojones about 10 years ago