Updated example data

Former-commit-id: b94593c

Author: cpwardell

exampledata/normal.bam

@@ -3,7 +3,7 @@
 ##source=strelka
 ##source_version=2.8.3
 ##startTime=Tue Oct 31 14:10:58 2017
-##cmdline=/illumina/pipeline/strelka/2.8.3/bin/configureStrelkaSomaticWorkflow.py --indelCandidates manta/results/variants/candidateSmallIndels.vcf.gz --normalBam /illumina/runs/yan_working_dir/genome_in_a_bottle/genome_in_a_bottle/merged_sorted_markdups/24385-200_AH5G7WCCXX_S4_L004_aligned.sorted.mark_dups.bam --tumorBam /illumina/runs/yan_working_dir/genome_in_a_bottle/genome_in_a_bottle/merged_sorted_markdups/24385-12878-30-200_aligned.sorted.mark_dups.bam --referenceFasta /illumina/genomes/Homo_sapiens/Ensembl/GRCh37_Release75/Sequence/WholeGenomeFasta/genome.fa --runDir strelka2
+##cmdline=/illumina/pipeline/strelka/2.8.3/bin/configureStrelkaSomaticWorkflow.py --indelCandidates manta/results/variants/candidateSmallIndels.vcf.gz --normalBam /illumina/runs/chris_working_dir/genome_in_a_bottle/genome_in_a_bottle/merged_sorted_markdups/24385-200_AH5G7WCCXX_S4_L004_aligned.sorted.mark_dups.bam --tumorBam /illumina/runs/chris_working_dir/genome_in_a_bottle/genome_in_a_bottle/merged_sorted_markdups/24385-12878-30-200_aligned.sorted.mark_dups.bam --referenceFasta /illumina/genomes/Homo_sapiens/Ensembl/GRCh37_Release75/Sequence/WholeGenomeFasta/genome.fa --runDir strelka2
 ##reference=file:///illumina/genomes/Homo_sapiens/Ensembl/GRCh37_Release75/Sequence/WholeGenomeFasta/genome.fa
 ##contig=<ID=1,length=249250621>
 ##contig=<ID=2,length=243199373>

exampledata/normal.bam.REMOVED.git-id

@@ -1,10 +1,16 @@
 #!/bin/bash
 
 ## Examples of how to run FiNGS on the example data, with number of PASSing variants for each
-python3 ../FiNGS.py -n normal.bam -t tumor.bam -v s2.raw.vcf --PASSonlyin --PASSonlyout --overwrite # 16 PASS
+
+## Recommended settings
+python3 ../FiNGS.py -n normal.bam -t tumor.bam -v s2.raw.vcf --PASSonlyin --PASSonlyout # 16 PASS
+
+## ICGC mode
+#python3 ../FiNGS.py -n normal.bam -t tumor.bam -v s2.raw.vcf -r /path/to/reference/genome.fa --PASSonlyin --PASSonlyout --ICGC # 23 PASS
+
+## Other options
 #python3 ../FiNGS.py -n normal.bam -t tumor.bam -v s2.raw.vcf --PASSonlyin # 16 PASS, 38 total
 #python3 ../FiNGS.py -n normal.bam -t tumor.bam -v s2.raw.vcf --PASSonlyout # 20 PASS
 #python3 ../FiNGS.py -n normal.bam -t tumor.bam -v s2.raw.vcf # 20 PASS, 1207 total
 
-## ICGC mode
-#python3 ../FiNGS.py -n normal.bam -t tumor.bam -v s2.raw.vcf -r /path/to/reference/genome.fa --PASSonlyin --PASSonlyout --ICGC # 23 PASS
+

exampledata/normal.bai exampledata/normal.bam.baiexampledata/normal.bai renamed to exampledata/normal.bam.bai

@@ -14,8 +14,6 @@
 import statsmodels.nonparametric.api as smnp
 import matplotlib.backends.backend_pdf
 
-#matplotlib.use('Agg') # Allows plotting without X-server; must be done before importing matplotlib.pyplot
-
 from matplotlib import pyplot
 from collections import OrderedDict
 from itertools import repeat, product
@@ -129,8 +127,6 @@ def applyfilters(tdata,ndata,sdata,pdict,resultsdir,vcfpath,referencegenome,PASS
 def filterplotter(tdata,ndata,fdata,pdict,sdict,resultsdir):
     ## Read in tdata and ndata
     try:
-        #tdf = pandas.read_csv(tdata, compression='gzip', sep="\t", header=None, names=cnames)
-        #ndf = pandas.read_csv(ndata, compression='gzip', sep="\t", header=None, names=cnames)
         tdf = pandas.read_csv(tdata, compression='gzip', sep="\t", header=0)
         ndf = pandas.read_csv(ndata, compression='gzip', sep="\t", header=0)