Merge pull request #21 from CEGRcode/revisions

Updates responding to reviewer comments

Author: owlang

.gitignore

@@ -1,30 +1,12 @@
 **/.DS_Store
-EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa
-EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.amb
-EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.ann
-EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.bwt
-EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.pac
-EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.sa
-EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.1.bt2
-EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.2.bt2
-EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.3.bt2
-EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.4.bt2
-EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.rev.1.bt2
-EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa.rev.2.bt2
-EpitopeID/ecoli_EpiID/FASTA_genome/genome.fa.amb
-EpitopeID/ecoli_EpiID/FASTA_genome/genome.fa.ann
-EpitopeID/ecoli_EpiID/FASTA_genome/genome.fa.bwt
-EpitopeID/ecoli_EpiID/FASTA_genome/genome.fa.pac
-EpitopeID/ecoli_EpiID/FASTA_genome/genome.fa.sa
-EpitopeID/hg19_EpiID/FASTA_genome/genome.fa
-EpitopeID/hg19_EpiID/FASTA_genome/genome.fa.amb
-EpitopeID/hg19_EpiID/FASTA_genome/genome.fa.ann
-EpitopeID/hg19_EpiID/FASTA_genome/genome.fa.bwt
-EpitopeID/hg19_EpiID/FASTA_genome/genome.fa.pac
-EpitopeID/hg19_EpiID/FASTA_genome/genome.fa.sa
-EpitopeID/hg19_EpiID/FASTA_genome/genome.fa.1.bt2
-EpitopeID/hg19_EpiID/FASTA_genome/genome.fa.2.bt2
-EpitopeID/hg19_EpiID/FASTA_genome/genome.fa.3.bt2
-EpitopeID/hg19_EpiID/FASTA_genome/genome.fa.4.bt2
-EpitopeID/hg19_EpiID/FASTA_genome/genome.fa.rev.1.bt2
-EpitopeID/hg19_EpiID/FASTA_genome/genome.fa.rev.2.bt2
+EpitopeID/ecoli_EpiID/FASTA_genome/genome.fa.*
+EpitopeID/sacCer3_EpiID/FASTA_genome/genome.fa*
+EpitopeID/hg19_EpiID/FASTA_genome/genome.fa*
+EpitopeID/hg19_EpiID_v2/FASTA_genome/genome.fa*
+StrainID/hg38_VCF
+StrainID/hg38_ENCODE
+StrainID/hg38_DepMap
+StrainID/utility_scripts/header.vcf
+StrainID/utility_scripts/CL_names.txt
+StrainID/utility_scripts/CSV
+StrainID/utility_scripts/hg38_DepMap

DeletionID/delScripts/detect_deletion_BAM.py

@@ -15,7 +15,7 @@
 Log2 output minimum threshold (Default -3)		-l Log2_Threshold
 Mappability threshold to consider (Default 0.25)	-M Mappability_%
 
-Example: python2 detect_deletion_BAM.py -b NGS.bam -c Interval.bed -m Mappability.tab -o NGS_deletion.tab -l -2 -M 0.25
+Example: python detect_deletion_BAM.py -b NGS.bam -c Interval.bed -m Mappability.tab -o NGS_deletion.tab -l -2 -M 0.25
 """
 
 def calculateDeletion(PASS):