eugenefischer 856063529b Read depth simulation is now compatible with plate caching

2022-09-28 12:47:00 -05:00

..

META-INF

Add .jar manifest to repo

2022-02-22 21:45:46 -06:00

BiGpairSEQ.java

revert options menu

2022-09-26 14:24:58 -05:00

CellFileReader.java

Refactor sequences to be strings instead of integers, to make simulating read errors easier

2022-09-26 13:37:48 -05:00

CellFileWriter.java

Refactor sequences to be strings instead of integers, to make simulating read errors easier

2022-09-26 13:37:48 -05:00

CellSample.java

Refactor sequences to be strings instead of integers, to make simulating read errors easier

2022-09-26 13:37:48 -05:00

CommandLineInterface.java

Refactor to simplify graph creation code

2022-09-28 00:07:59 -05:00

Equations.java

make everything use same random number generator

2022-02-23 09:29:21 -06:00

GraphDataObjectReader.java

Add detail to error message

2022-03-01 15:24:14 -06:00

GraphDataObjectWriter.java

Control verbose output

2022-02-27 16:03:57 -06:00

GraphMLFileWriter.java

Add read depth attributes to graphml output

2022-09-28 03:01:52 -05:00

GraphModificationFunctions.java

spacing

2022-09-26 23:38:56 -05:00

GraphWithMapData.java

Add read depth parameters to output metadata

2022-09-27 11:13:12 -05:00

HeapType.java

make heap type an enum

2022-02-26 08:15:31 -06:00

InteractiveInterface.java

Read depth simulation is now compatible with plate caching

2022-09-28 12:47:00 -05:00

MatchingFileWriter.java

Implemented storing graphs in memory for multiple pairing experiments

2022-02-22 21:30:00 -06:00

MatchingResult.java

clean up metadata

2022-09-27 12:15:12 -05:00

Plate.java

Reorder conditional

2022-09-28 00:57:06 -05:00

PlateFileReader.java

Refactor sequences to be strings instead of integers, to make simulating read errors easier

2022-09-26 13:37:48 -05:00

PlateFileWriter.java

Refactor sequences to be strings instead of integers, to make simulating read errors easier

2022-09-26 13:37:48 -05:00

SequenceRecord.java

Make serializable and implement getWellOccupancies method

2022-09-28 00:58:02 -05:00

SequenceType.java

Hand-merge of some things from Dev_Vertex branch that didn't make it in for some reason

2022-09-25 19:07:25 -05:00

Simulator.java

Remove redundant toString() calls

2022-09-28 02:08:17 -05:00

Vertex.java

Refactor Vertex class to use SequenceRecords

2022-09-28 00:58:44 -05:00