Tags

0.5

## v0.5 (260915ac)
+  faster running times (new CIGAR parsing without regex, new implementation for static methods logGamma and pmfGP)
+  aligned reads of length < 8 are never considered
+  now handles hard clipping for secondary alignments (provided that SAM col. 10 and 11 are not empty)
+  fixed bug when reading low-Phreded bases (sometimes yielding slightly different results in comparison with v0.4)
+  output tsv file now contains a new col. 11 (named 'clip') containing the number of read clips at each position

0.4

v0.4 (260214ac)
+  new metrics FUc, i.e. Fraction of the genome Under the coverage cutoff c = 10x, 20x, ..., 50x
+  Gompertz function weigthing discarded in lsGP method
+  fixed bugs in pmfGP method
+  slight modification in fitGP method (e.g. starting values)
+  replacement of the Q-Q plot R2 with the Bhattacharyya coefficient BC
+  new option -c to better assess multi-allelic positions
+  option -f is now only dedicated to the inference of the degenerated nucleotide for each multi-allelic position

0.3

v0.3 (251128ac)
+  momo computation now starts at x = 1 to avoid the effect of non-covered positions (if any)
+  every enhanced contig that contains only non-ACGT residues are not returned
+  improved fitGP method by constraining lambda > 0 and theta < 1
+  improved fitGP method when theta ~ 0 by using an alternative tstep definition
+  improved fitGP method by using a wider range of div values
+  improved lsGP method by weigthing with a Gompertz function

0.2

## v0.2 (251119ac)
+  new default value: -Q 0
+  new option -s to allow secondary alignments (default: not set)
+  new option -V to print version
+  average (avg) and mean of the observed and theoretical distributions, resp., added in txt outfile
+  edited usage
+  optimized switch case on ACGT (using constant variable UP)
+  ability to read multiple SAM files via stdin, i.e. cat *.sam | CoPro [options]

0.1