Funcotator: suppress a log message about b37 contigs when not doing b37/hg19 conversion #8758
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…37/hg19 conversion Don't print the very long and misleading "The following contigs are present in b37 and missing in the input VCF sequence dictionary" log message when we're not even doing b37/hg19 conversion.
jamesemery
approved these changes
Apr 1, 2024
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Don't print the very long and misleading "The following contigs are present in b37 and missing in the input VCF sequence dictionary" log message when we're not even doing b37/hg19 conversion.
Users are getting log messages like this even when they have an hg38 dictionary:
16:21:32.764 INFO FuncotatorUtils - The following contigs are present in b37 and missing in the input VCF sequence dictionary:
16:21:32.767 INFO FuncotatorUtils - 1 (len=249250621,assembly=GRCh37)
16:21:32.767 INFO FuncotatorUtils - 2 (len=243199373,assembly=GRCh37)
16:21:32.767 INFO FuncotatorUtils - 3 (len=198022430,assembly=GRCh37)
16:21:32.767 INFO FuncotatorUtils - 4 (len=191154276,assembly=GRCh37)
16:21:32.767 INFO FuncotatorUtils - 5 (len=180915260,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 6 (len=171115067,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 7 (len=159138663,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 8 (len=146364022,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 9 (len=141213431,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 10 (len=135534747,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 11 (len=135006516,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 12 (len=133851895,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 13 (len=115169878,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 14 (len=107349540,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 15 (len=102531392,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 16 (len=90354753,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 17 (len=81195210,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 18 (len=78077248,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 19 (len=59128983,assembly=GRCh37)
16:21:32.768 INFO FuncotatorUtils - 20 (len=63025520,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - 21 (len=48129895,assembly=GRCh37)
16:21:32.769 INFO FuncotatorUtils - 22 (len=51304566,assembly=GRCh37)
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