Class 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()