reference statistics in stats output (fixes #2139)#2224
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Based on review, removed the unnecessary option argument in ref-stats. |
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Updated man page based on review suggestions. |
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Fixes #2139.
Reference statistics is calculated and added to stats output.
It calculates the length from header and region specifications and doesn't need reference file for it.
GC content and unknown base counts are calculated when ref. file is provided and will have -1 when it is not provided.
1st line in RFS section gives the total sequence count in input file, count of regions in status, average GC, min, max, average and total counts.
2nd line onwards gives regions, lengths, GC and unknown base count.
Regions are selected based on options, it is given by target when -t is used and given by region specification when -t is not there. All targets in input file is used when neither -t and region spec are present.