#==========
# Abstract:
#==========

Title:
  Continuous Wavelet Dynamic Time Warping for unbalanced global mapping in nanopore sequencing analysis

Author:
  Renmin Han,
  Yu Li,
  Xin Gao,
  Sheng Wang

Contact email:
  xin.gao@kaust.edu.sa
  realbigws@gmail.com

Reference:
   https://academic.oup.com/bioinformatics/article-abstract/34/17/i722/5093233



#=========
# Install:
#=========

./install.sh


#=======
# Usage:
#=======

#---- type ----#
./cwDTW_nano -h


#---- usage ---#
----------- cwDTW_nano ----------
version v0.13 (FEB 28 2018)
-------------------------------------------------------------
required:
[-i DNA SEQUENCE][-p NANO SIGNAL][-o OUTPUT]
optional:
([-r RADIUS])([-l LEVEL])([-s SCALE])([-k kmer])([-R RNA])
-------------------------------------------------------------
**** required: ******
DNA SEQUENCE: (reference) sequence, such as ATCG...;
NANO SIGNAL:   (nanopore) raw electrical current signal;
OUTPUT:   nano signal labeling result; if not specified, then no output be generated;
**** key parameters: ******
RADIUS:   warp search radius (default 50);
LEVEL:    sampling level in continous wavelet (default 3);
SCALE:    base scale in continous wavelet (default sqrt(2));
kmer:     kmer pore model. 0 for 5mer; 1 for 6mer (default 0);
RNA:      RNA pore model or not. 0 for DNA, 1 for 200mv RNA, -1 for 180mv RNA (default 0);



#=========
# Example:
#=========

#---- align DNA sequence and nanopore raw signal ------#
./cwDTW_nano -i example/002a08b9-0248-4929-9759-2d5c0942076d.fasta -p example/002a08b9-0248-4929-9759-2d5c0942076d.rawsig -o align_out


-------
[Note]:
-------
The input DNA sequence should only contain 'A','T','C', and 'G' nucleotide.



#===============
# Output format:
#===============

e.g., {k}=5

   1     2             3         4            5                6                             7          8
------------------------------------------------------------------------------------------------------------
  550   640 |          1          1 |         1.04565        -1.17484          diff:        2.22049   GGAAA
  433   512 |          2          2 |       -0.560209       -0.531815          diff:       0.028394   GAAAA
  411     1 |          3          3 |       -0.862165        -1.09529          diff:        0.23312   AAAAC
  409     1 |          4          3 |       -0.889616        -1.09529          diff:        0.20567   AAAAC
  408     1 |          5          3 |       -0.903341        -1.09529          diff:       0.191944   AAAAC
  389     1 |          6          3 |        -1.16412        -1.09529          diff:      0.0688361   AAAAC
  389     1 |          7          3 |        -1.16412        -1.09529          diff:      0.0688361   AAAAC
  377     1 |          8          3 |        -1.32883        -1.09529          diff:        0.23354   AAAAC
  391     1 |          9          3 |        -1.13667        -1.09529          diff:      0.0413855   AAAAC



---------
[Legend]:
---------
the 1st column is the raw signal value,
the 2nd column is the k-mer ID 
  (see [MAP] for the mapping between k-mer DNA and k-mer ID),

the 3rd column shows the mapping of the first position (i.e., on raw signal) starting from 1,
the 4th column shows the mapping of the second position (i.e., on DNA sequence) starting from 1,

the 5th column indicates the Z-normalized value of raw signal,
the 6th column indicates the Z-normalized value of genome translated signal 
  (see [VAL] for the translated signal of each k-mer),

the 7th column illustrates the absolute difference between the two Z-normalized values.
the 8th column is the kmer for labeling.


-------
[Note]:
-------
please find [MAP] in 'src/kmer/{k}mer_index_mapping'
please find [VAL] in 'src/kmer/{k}mer_index_official.rc'