EmpiricalSNPCalling_v1.4.4

1.4.4

• Make BarcodeFaker task work for input files that do not finish with .fasta or .fq
• Adapt BarcodeFaker required memory and time
• Adapt STACKs required memory

EmpiricalReads2Map_v1.5.1

1.5.1

• Make EmpiricalMaps for polyploids compatible with Reads2MapApp v0.0.2
• Polyploid map quality diagnostic by resampling
• Adapt regenotyping memory usage
• Make BarcodeFaker task work for input files that do not finish with .fasta or .fq
• Adapt BarcodeFaker required memory and time
• Adapt STACKs required memory

EmpiricalMaps_v1.3.1

1.3.1

• Make EmpiricalMaps for polyploids compatible with Reads2MapApp v0.0.2
• Polyploid map quality diagnostic by resampling
• Adapt regenotyping memory usage

SimulatedReads2Map_develop

1.0.2

• more flexibility to choose the probability to be used in the HMM:

• new parameters:

• global_errors: array with global errors to be tested
• genoprob_error: boolean defining if software probabilities should be tested
• genoprob_global_errors: array with global errors to be tested together with the software probabilities following: 1 - (1 - global error) x (1 - software error probability)

PreprocessingReads_develop

1.0.1

• runtimes adapted to run with Caper

EmpiricalSNPCalling_develop

1.4.4

• Make BarcodeFaker task work for input files that do not finish with .fasta or .fq
• Adapt BarcodeFaker required memory and time
• Adapt STACKs required memory

EmpiricalReads2Map_develop

1.5.1

• Make EmpiricalMaps for polyploids compatible with Reads2MapApp v0.0.2
• Polyploid map quality diagnostic by resampling
• Adapt regenotyping memory usage
• Make BarcodeFaker task work for input files that do not finish with .fasta or .fq
• Adapt BarcodeFaker required memory and time
• Adapt STACKs required memory

EmpiricalMaps_develop

1.3.1

• Make EmpiricalMaps for polyploids compatible with Reads2MapApp v0.0.2
• Polyploid map quality diagnostic by resampling
• Adapt regenotyping memory usage

EmpiricalSNPCalling_v1.4.3

1.4.3

• Adapt tassel and stacks tasks also for polyploids
• Update tests

EmpiricalReads2Map_v1.5.0

1.5.0

• Adapt tassel and stacks tasks also for polyploids
• Update tests
• Add MAPpoly new functions framework_map and update_framework_map
• Polyploid analysis output compatible with Reads2MapApp v0.0.1
• Remove LargeList deprecated package as dependency