56e876a710840529715cd8a5496f46e3e9d372cb max Fri Aug 21 03:57:10 2020 -0700 fixing general usage problems with chromToUcsc found by Matt, refs diff --git src/utils/chromToUcsc/tests/hg19.chromAlias.tsv src/utils/chromToUcsc/tests/hg19.chromAlias.tsv index 3170ef7..2abecab 100644 --- src/utils/chromToUcsc/tests/hg19.chromAlias.tsv +++ src/utils/chromToUcsc/tests/hg19.chromAlias.tsv @@ -1,16 +1,15 @@ -alias chrom source 1 chr1 assembly CM000663.1 chr1 genbank NC_000001.10 chr1 refseq 10 chr10 assembly CM000672.1 chr10 genbank NC_000010.10 chr10 refseq GL383543.1 chr10_gl383543_fix genbank HG544_PATCH chr10_gl383543_fix assembly NW_003315932.1 chr10_gl383543_fix refseq GL383544.1 chr10_gl383544_fix genbank HG995_PATCH chr10_gl383544_fix assembly NW_003315933.1 chr10_gl383544_fix refseq GL383545.1 chr10_gl383545_alt genbank HSCHR10_1_CTG2 chr10_gl383545_alt assembly NW_003315934.1 chr10_gl383545_alt refseq @@ -678,30 +677,33 @@ JH636059.1 chr9_jh636059_fix genbank NW_003871067.1 chr9_jh636059_fix refseq HG1500_PATCH chr9_jh806577_fix assembly JH806577.1 chr9_jh806577_fix genbank NW_004070867.1 chr9_jh806577_fix refseq HG1501_PATCH chr9_jh806578_fix assembly JH806578.1 chr9_jh806578_fix genbank NW_004070868.1 chr9_jh806578_fix refseq HG1502_PATCH chr9_jh806579_fix assembly JH806579.1 chr9_jh806579_fix genbank NW_004070869.1 chr9_jh806579_fix refseq HG50_PATCH chr9_kb663605_fix assembly KB663605.1 chr9_kb663605_fix genbank NW_004504301.1 chr9_kb663605_fix refseq NC_001807.4 chrM genbank +J01415.2 chrMT genbank +MT chrMT assembly +NC_012920.1 chrMT refseq GL000211.1 chrUn_gl000211 genbank HSCHRUN_RANDOM_CTG1 chrUn_gl000211 assembly NT_113961.1 chrUn_gl000211 refseq GL000212.1 chrUn_gl000212 genbank HSCHRUN_RANDOM_CTG2 chrUn_gl000212 assembly NT_113923.1 chrUn_gl000212 refseq GL000213.1 chrUn_gl000213 genbank HSCHRUN_RANDOM_CTG3 chrUn_gl000213 assembly NT_167208.1 chrUn_gl000213 refseq GL000214.1 chrUn_gl000214 genbank HSCHRUN_RANDOM_CTG4 chrUn_gl000214 assembly NT_167209.1 chrUn_gl000214 refseq GL000215.1 chrUn_gl000215 genbank HSCHRUN_RANDOM_CTG5 chrUn_gl000215 assembly NT_167210.1 chrUn_gl000215 refseq