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| camelSampleTable | ampliQueso sample data |
| camelTest | camelTest - calculating permutation tests for camel measures (sequential and parallel versions) |
| compareCoverages | compareCoverages - camel measure for a single comparison. |
| compareCoveragesReg | compareCoveragesReg - calculating given camel measures for a list of regions specified by a BED file (sequential and parallel versions) |
| getCountTable | getCountTable - obtaining typical count table. |
| getSNP | getSNP - finding SNPs in all samples for regions specified by a BED file all regions if BED file not provided (sequential and parallel versions) |
| ndMax | ampliQueso sample data |
| ndMin | ampliQueso sample data |
| runAQReport | runAQReport - runing the AmpliQueso report |