2014-01-23

Modification in 5.0.1

countMappedReads.py

1. Remove the 30bp intron-exon boundary condition in calculating the coverage
2. Generate max coverage file to record the max overall reads coverage in each exon
3.  Do not generate filter reads any more.
4. Sort all individual reference with max overall reads coverage, then pickup the top 200.

HLA_parts.sh

1. Do not remove the scratch directory

map_single.sh

1. Do not remove the scratch directory

select_single.sh

 1. Remove filtered reads location as input parameters

runTyping.py

1. use /BioScratch/zfu as scratch dir
2. no filtered reads parameters
3. use one countMappedReads.py for all classes

/Bioinformatics/Users/zfu/HLA_Typing/HLA_cDNA_Database/IMGT.Release.3.12.0/Index.Test.Single

Only kept alleles with 2-digits subtype name