add test for vep stats

public/biopet-extensions/src/test/resources/vep.metrics

+[VEP run statistics]
+VEP version (API)	77 (77)
+Cache/Database	/usr/local/Genomes/H.Sapiens/hg19/vep_cache_75/homo_sapiens/75
+Species	homo_sapiens
+Command line options	-i test.vcf -o test.vep.vcf -v --everything --stats_text --cache --vcf --allow_non_variant --species homo_sapiens --dir /usr/local/Genomes/H.Sapiens/hg19/vep_cache_75 --fasta /usr/local/Genomes/H.Sapiens/hg19/vep_cache_75/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa --fork 2 --cache_version 75 --db_version 75 --failed 1 --offline
+Start time	2016-03-03 14:37:44
+End time	2016-03-03 14:37:54
+Run time	10 seconds
+Input file (format)	test.vcf (VCF)
+Output file	test.vep.vcf [text]
+
+[General statistics]
+Lines of input read	1000
+Variants processed	874
+Variants remaining after filtering	874
+Lines of output written	874
+Novel / existing variants	105 (12.0%) / 769 (88.0%)
+Overlapped genes	132
+Overlapped transcripts	661
+Overlapped regulatory features	164
+
+[Variant classes]
+insertion	29
+deletion	51
+SNV	794
+
+[Consequences (most severe)]
+splice_donor_variant	3
+frameshift_variant	1
+inframe_insertion	2
+inframe_deletion	1
+missense_variant	39
+splice_region_variant	11
+synonymous_variant	46
+5_prime_UTR_variant	19
+3_prime_UTR_variant	36
+non_coding_transcript_exon_variant	95
+intron_variant	518
+upstream_gene_variant	48
+downstream_gene_variant	27
+intergenic_variant	28
+
+[Consequences (all)]
+splice_donor_variant	6
+frameshift_variant	2
+inframe_insertion	15
+inframe_deletion	6
+missense_variant	101
+splice_region_variant	60
+synonymous_variant	173
+coding_sequence_variant	1
+5_prime_UTR_variant	33
+3_prime_UTR_variant	108
+non_coding_transcript_exon_variant	279
+intron_variant	3311
+NMD_transcript_variant	437
+non_coding_transcript_variant	1102
+upstream_gene_variant	1486
+downstream_gene_variant	1779
+TF_binding_site_variant	12
+feature_elongation	97
+regulatory_region_variant	253
+feature_truncation	278
+intergenic_variant	28
+
+[Coding consequences]
+frameshift_variant	2
+inframe_insertion	15
+inframe_deletion	6
+missense_variant	101
+synonymous_variant	173
+coding_sequence_variant	1
+
+[SIFT summary]
+deleterious	22
+tolerated	76
+
+[PolyPhen summary]
+possibly damaging	7
+unknown	12
+probably damaging	12
+benign	70
+
+[Variants by chromosome]
+1	874
+
+[Distribution of variants on chromosome 1]
+0	225
+1	407
+2	242
+3	0
+4	0
+5	0
+6	0
+7	0
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+
+[Position in protein]
+00-10%	29
+10-20%	63
+20-30%	34
+30-40%	20
+40-50%	23
+50-60%	25
+60-70%	31
+70-80%	11
+80-90%	32
+90-100%	30

public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictorTest.scala

+package nl.lumc.sasc.biopet.extensions
+
+import java.io.File
+import java.nio.file.Paths
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+  * Created by ahbbollen on 3-3-16.
+  */
+class VariantEffectPredictorTest extends TestNGSuite with Matchers {
+
+
+  @Test
+  def testSummaryStats = {
+    val file = new File(Paths.get(getClass.getResource("/vep.metrics").toURI).toString)
+
+    val vep = new VariantEffectPredictor(null)
+    val stats = vep.parseStatsFile(file)
+
+    stats.contains("VEP_run_statistics") shouldBe true
+    stats.contains("General_statistics") shouldBe true
+    stats.contains("Consequences_(most_severe)") shouldBe true
+    stats.contains("Consequences_(all)") shouldBe true
+    stats.contains("Coding_consequences") shouldBe true
+    stats.contains("SIFT_summary") shouldBe true
+    stats.contains("PolyPhen_summary") shouldBe true
+    stats.contains("Variants_by_chromosome") shouldBe true
+    stats.contains("Distribution_of_variants_on_chromosome_1") shouldBe true
+    stats.contains("Position_in_protein") shouldBe true
+
+
+  }
+
+}