Improve isotopologues extraction with XIC algorithm

[rolivella]

1) Extend bash script (https://github.com/coreforlife/c4lProteomics/blob/master/RawFileReader-XIC-json/runme.bash) to read output json (https://github.com/coreforlife/c4lProteomics/blob/master/RawFileReader-XIC-json/fgcz-xic.cs) and extract all isotopologues intensities.

2) Modify pipeline: replace module_parameter_QC_pepArea.knwf for this new bash script.

[rolivella]

Precode:

Code at: /home/rolivella/rawFileReader/xic/RawFileReader-XIC-json

1) Prepare input data: update masses.txt with all isotopologues masses. 2) Perform XIC from cpanse. A json is obtained with a list of masses, RT and intensities. 3) Search lighter isotopologues:

• Load and store the XIC json file.
• For each heavy isotopologue, a RTmax is obtained with Imax.
• Search in output XIC hashmap, for each lighter isotopologue and within RTmax windows, the most intense peak.

[rolivella]

Needed functions for a bash script:

1) Store generic JSON in a hash table. 2) Fancy search in a hash table.

[rolivella]

• At the moment I created a new branch to implement the new XIC QC03 calculations: https://github.com/proteomicsunitcrg/qcloud2-pipeline/tree/fgcz-xic
• I raised this issue to Christian and I closed it: https://github.com/coreforlife/c4lProteomics/issues/9

[rolivella]

I close this issue, script finished.