Class TestCasesVcf


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

      • TestCasesVcf

        public TestCasesVcf()
    • Method Detail

      • test_00

        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

        public void test_01()
        Basic parsing
      • test_04_del

        public void test_04_del()
        Deletions
      • test_05_choking_on_dot_slash_dot

        public void test_05_choking_on_dot_slash_dot()
        Problems parsing
      • test_06_mixed_change

        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

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

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

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

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

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

        public void test_12_readHeader()
      • test_12_readHeader_NL

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

        public void test_13_chrOri()
      • test_14_VcfInfoKey

        public void test_14_VcfInfoKey()
      • test_14_VcfInfoValue

        public void test_14_VcfInfoValue()
      • test_15_Eff_format_version_guess

        public void test_15_Eff_format_version_guess()
      • test_16_indels

        public void test_16_indels()
      • test_18_vcf_tabix

        public void test_18_vcf_tabix()
      • test_22_huge_headers

        public void test_22_huge_headers()
      • test_23_VcfUnsorted

        public void test_23_VcfUnsorted()
      • test_24_VcfEffect_parse_SO

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

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

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

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

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

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

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

        public void test_31_MISSING_REF()
      • test_32_VcfInfoKeyNames

        public void test_32_VcfInfoKeyNames()
      • test_33_translocations

        public void test_33_translocations()
      • test_34_vcfInfoEncoding

        public void test_34_vcfInfoEncoding()
      • test_35_translocations_parsing

        public void test_35_translocations_parsing()