Class TestCasesVcf

java.lang.Object
org.snpeff.snpEffect.testCases.unity.TestCasesBase
org.snpeff.snpEffect.testCases.unity.TestCasesVcf

public class TestCasesVcf extends TestCasesBase
VCF parsing test cases
Author:
pcingola
  • Constructor Details

    • TestCasesVcf

      public TestCasesVcf()
  • Method Details

    • test_00

      @Test public void test_00()
      Check that the size is correct (at least for SNPs)

      Louis Letourneau discovered this horrendous bug. This is my first attempt to fix it....

    • test_01

      @Test public void test_01()
      Basic parsing
    • test_04_del

      @Test public void test_04_del()
      Deletions
    • test_05_choking_on_dot_slash_dot

      @Test public void test_05_choking_on_dot_slash_dot()
      Problems parsing
    • test_06_mixed_change

      @Test public void test_06_mixed_change()
      Problems creating variants

      The problem is when creating a variant from this line: Chr1 223919 . CTCGACCACTGGAA CTCACATCCATACAT,CATGACCACTGGAA

      There are two changes: CTCGACCACTGGAA CTCACATCCATACAT => GACCACTGGAA / ACATCCATACAT (Mixed change?)

      CTCGACCACTGGAA CATGACCACTGGAA ^^ => CG / TG (MNP)

    • test_07_long_lines

      @Test public void test_07_long_lines()
      Extremely weird long lines in a VCF file (thousands of bases long)
    • test_08_alt_del

      @Test public void test_08_alt_del()
      Test for "" in ALT field
    • test_09_empty_ALT

      @Test public void test_09_empty_ALT()
      Empty ALT: Not a variant
    • test_10_empty_QUAL

      @Test public void test_10_empty_QUAL()
      Empty Quality: Not a variant
    • test_11_empty

      @Test public void test_11_empty()
      Empty fields should show '.' when printed
    • test_12_readHeader

      @Test public void test_12_readHeader()
    • test_12_readHeader_NL

      @Test public void test_12_readHeader_NL()
      Header should NOT have a trailing '\n'
    • test_13_chrOri

      @Test public void test_13_chrOri()
    • test_14_VcfInfoKey

      @Test public void test_14_VcfInfoKey()
    • test_14_VcfInfoValue

      @Test public void test_14_VcfInfoValue()
    • test_15_Eff_format_version_guess

      @Test public void test_15_Eff_format_version_guess()
    • test_16_indels

      @Test public void test_16_indels()
    • test_18_vcf_tabix

      @Test public void test_18_vcf_tabix()
    • test_22_huge_headers

      @Test public void test_22_huge_headers()
    • test_23_VcfUnsorted

      @Test public void test_23_VcfUnsorted()
    • test_24_VcfEffect_parse_SO

      @Test public void test_24_VcfEffect_parse_SO()
      Parsing effect that created an exception (going from SO -> Classic)
    • test_25_Genomic_VCF

      @Test public void test_25_Genomic_VCF()
      Parsing Genomic VCFs http://www.broadinstitute.org/gatk/guide/article?id=4017
    • test_26_vcfInfoHeaderAdd

      @Test public void test_26_vcfInfoHeaderAdd()
      Add a new INFO and the respective header
    • test_27_vcfInfoHeaderReplace

      @Test public void test_27_vcfInfoHeaderReplace()
      Add and replace an INFO header
    • test_28_vcfInfoReplace

      @Test public void test_28_vcfInfoReplace()
      Add and replace an INFO header
    • test_29

      @Test public void test_29()
      Test old effect separator '+' instead of '&'
    • test_30_gVCF_NON_REF

      @Test public void test_30_gVCF_NON_REF()
      Non-variant gVCF entries (i.e. ALT=)
    • test_31_MISSING_REF

      @Test public void test_31_MISSING_REF()
    • test_32_VcfInfoKeyNames

      @Test public void test_32_VcfInfoKeyNames()
    • test_33_translocations

      @Test public void test_33_translocations()
    • test_34_vcfInfoEncoding

      @Test public void test_34_vcfInfoEncoding()
    • test_35_translocations_parsing

      @Test public void test_35_translocations_parsing()
    • test_36_cleanupUnderscores

      @Test public void test_36_cleanupUnderscores()