Forgot to save unmapped reads?

Forgot to save unmapped reads, we got you covered. Use --digGold and -a options

For example:

python imrep.py --digGold -a example/toyExample_allReads.fastq example/toyExample_onlyMapped.bam example/toyExample.cdr3 

This is expected output

Parse fastq file with orignal raw reads (all reads) and extract the unmapped reads
Number of reads extacted from  IGH locus :  0
Number of reads extacted from  IGK locus :  0
Number of reads extacted from  IGL locus :  0
Number of reads extacted from  TRA locus :  0
Number of reads extacted from  TRB locus :  0
Number of reads extacted from  TRD locus :  0
Number of reads extacted from  TRG locus :  0
Parse bam file with mapped reads
Number of unmapped reads extracted 100
Starting ImReP-0.6 (developped by Igor Mandric, Serghei Mangul)


 _                          
(_)_ __ ___  _ __ ___ _ __  
| | '_ ` _ \| '__/ _ \ '_ \ 
| | | | | | | | |  __/ |_) |
|_|_| |_| |_|_|  \___| .__/ 
                     |_|    


5 partial-V CDR3 found
0 partial-J CDR3 found
8 full CDR3 found:
	- 8 of type IGH
	- 0 of type IGK
	- 0 of type IGL
	- 0 of type TRA
	- 0 of type TRB
	- 0 of type TRD
	- 0 of type TRG
Done. Bye-bye