EmpiricalMaps_v1.3.0

1.3.0

• Add MAPpoly new functions framework_map and update_framework_map
• Update tests
• Polyploid analysis output compatible with Reads2MapApp v0.0.1
• Remove LargeList deprecated package as dependency

EmpiricalSNPCalling_v1.4.2

1.4.2

• Update example for pair-end reads inputs

EmpiricalReads2Map_v1.4.3

1.4.3

• Update example for pair-end reads inputs

SimulatedReads2Map_v1.0.2

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)

EmpiricalSNPCalling_v1.4.1

1.4.1

• Use BCFtools norm to left-align indel marker positions identified by GATK, STACKs and freebayes

EmpiricalReads2Map_v1.4.2

1.4.2

• 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)

EmpiricalMaps_v1.2.5

1.2.5

• 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)

SimulatedReads2Map_v1.0.1

1.0.1

• runtimes adapted to run with Caper

PreprocessingReads_v1.0.1

1.0.1

• runtimes adapted to run with Caper

EmpiricalSNPCalling_v1.4.0

1.4.0

• STACKs included
• support to pair-end reads
• defined defaults
• runtimes adapted to run with Caper
• new tutorial