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Program Information

Name: BBMap
Domain: Bioinformatics
Functionality: BBMap is a bioinformatics toolkit that includes several alignment procedures. We specifically targeted the \textbf{BBMap.align
Input: We used the reads from a reference genome of E Coli strain 536, available from the USCS Microbial Genome Browser.
Output:

Reference

 Experiences of Testing Bioinformatics Programs for Detecting Subtle Faults https://doi.org/10.1145/2897676.2897678 

MR Information

MR1------Read Removal

Description:
Property: Half of the reads from the initial input collection are deleted. We expect the follow-up mappings to be a subset of the initial mappings since the reads should map to the same locations. We also expect the coverage in the follow-up test to be half of the original coverage.
Source input:
Source output:
Follow-up input:
Follow-up output:
Input relation:
Output relation:
Pattern:

MR2------Read Addition

Description:
Property: The reads in the initial test are duplicated, making the input for the follow-up test twice as large. We expect the follow-up sequencing coverage to be identical since the copied reads should map to the same locations as the originals.
Source input:
Source output:
Follow-up input:
Follow-up output:
Input relation:
Output relation:
Pattern:

MR3------Unmapped Reads 

Description:
Property: After the initial mapping is completed the modified input reads are created by selecting only the reads from the initial run that were not successfully mapped. We expect the follow-up test to map none of these reads. 
Source input:  
Source output:  
Follow-up input:  
Follow-up output:  
Input relation:  
Output relation:  
Pattern:

MR4------Mapped Reads 

Description:
Property: Similar to the Unmapped reads relation, but the reads selected are only those that were successfully mapped. We then expect the follow-up test to map every read. 
Source input:  
Source output:  
Follow-up input:  
Follow-up output:  
Input relation:  
Output relation:  
Pattern:

MR5------Read Permutation 

Description:
Property: The reads from the initial test are shuffled randomly. We expect this to have no effect on  the output mappings. 
Source input:  
Source output:  
Follow-up input:  
Follow-up output:  
Input relation:  
Output relation:  
Pattern:
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