Usage of muscato:
-BloomSize int
Size of Bloom filter, in bits
-ConfigFileName string
JSON file containing configuration parameters
-GeneFileName string
Gene file name (processed form)
-GeneIdFileName string
Gene ID file name (processed form)
-MMTol int
Number of mismatches allowed above best fit
-MatchMode string
'first' or 'best' (retain first/best 'MaxMatches' matches meeting criteria)
-MaxConfirmProcs int
Run this number of match confirmation processes concurrently
-MaxMatches int
Return no more than this number of matches per window
-MaxReadLength int
Reads longer than this length are truncated
-MinDinuc int
Minimum number of dinucleotides to check for match
-MinReadLength int
Reads shorter than this length are skipped
-NoCleanTemp
Do not delete temporary files from TempDir
-NumHash int
Number of hashses
-PMatch float
Required proportion of matching positions
-ReadFileName string
Sequencing read file (fastq format)
-ResultsFileName string
File name for results
-SortPar int
Number of parallel sort processes (default 8)
-SortTemp string
Directory to use for sort temp files
-TempDir string
Workspace for temporary files
-WindowWidth int
Width of each window
-Windows string
Starting position of each window