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nh13/michael_hoffmans_super_special_wishmaker.dict

Last active May 22, 2020 02:31
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Michael Hoffmans Super Special Wishmaker
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michael_hoffmans_super_special_wishmaker.dict
@HD VN:1.6
@SQ SN:chr1 LN:249250621 am:1 ga:CM000663.1 sn:1 ra:NC_000001.10 un:chr1 AN:1,CM000663.1,NC_000001.10 sr:assembled-molecule
@SQ SN:chr2 LN:243199373 am:2 ga:CM000664.1 sn:2 ra:NC_000002.11 un:chr2 AN:2,CM000664.1,NC_000002.11 sr:assembled-molecule
@SQ SN:chr3 LN:198022430 am:3 ga:CM000665.1 sn:3 ra:NC_000003.11 un:chr3 AN:3,CM000665.1,NC_000003.11 sr:assembled-molecule
@SQ SN:chr4 LN:191154276 am:4 ga:CM000666.1 sn:4 ra:NC_000004.11 un:chr4 AN:4,CM000666.1,NC_000004.11 sr:assembled-molecule
@SQ SN:chr5 LN:180915260 am:5 ga:CM000667.1 sn:5 ra:NC_000005.9 un:chr5 AN:5,CM000667.1,NC_000005.9 sr:assembled-molecule
@SQ SN:chr6 LN:171115067 am:6 ga:CM000668.1 sn:6 ra:NC_000006.11 un:chr6 AN:6,CM000668.1,NC_000006.11 sr:assembled-molecule
@SQ SN:chr7 LN:159138663 am:7 ga:CM000669.1 sn:7 ra:NC_000007.13 un:chr7 AN:7,CM000669.1,NC_000007.13 sr:assembled-molecule
@SQ SN:chr8 LN:146364022 am:8 ga:CM000670.1 sn:8 ra:NC_000008.10 un:chr8 AN:8,CM000670.1,NC_000008.10 sr:assembled-molecule
@SQ SN:chr9 LN:141213431 am:9 ga:CM000671.1 sn:9 ra:NC_000009.11 un:chr9 AN:9,CM000671.1,NC_000009.11 sr:assembled-molecule
@SQ SN:chr10 LN:135534747 am:10 ga:CM000672.1 sn:10 ra:NC_000010.10 un:chr10 AN:10,CM000672.1,NC_000010.10 sr:assembled-molecule
@SQ SN:chr11 LN:135006516 am:11 ga:CM000673.1 sn:11 ra:NC_000011.9 un:chr11 AN:11,CM000673.1,NC_000011.9 sr:assembled-molecule
@SQ SN:chr12 LN:133851895 am:12 ga:CM000674.1 sn:12 ra:NC_000012.11 un:chr12 AN:12,CM000674.1,NC_000012.11 sr:assembled-molecule
@SQ SN:chr13 LN:115169878 am:13 ga:CM000675.1 sn:13 ra:NC_000013.10 un:chr13 AN:13,CM000675.1,NC_000013.10 sr:assembled-molecule
@SQ SN:chr14 LN:107349540 am:14 ga:CM000676.1 sn:14 ra:NC_000014.8 un:chr14 AN:14,CM000676.1,NC_000014.8 sr:assembled-molecule
@SQ SN:chr15 LN:102531392 am:15 ga:CM000677.1 sn:15 ra:NC_000015.9 un:chr15 AN:15,CM000677.1,NC_000015.9 sr:assembled-molecule
@SQ SN:chr16 LN:90354753 am:16 ga:CM000678.1 sn:16 ra:NC_000016.9 un:chr16 AN:16,CM000678.1,NC_000016.9 sr:assembled-molecule
@SQ SN:chr17 LN:81195210 am:17 ga:CM000679.1 sn:17 ra:NC_000017.10 un:chr17 AN:17,CM000679.1,NC_000017.10 sr:assembled-molecule
@SQ SN:chr18 LN:78077248 am:18 ga:CM000680.1 sn:18 ra:NC_000018.9 un:chr18 AN:18,CM000680.1,NC_000018.9 sr:assembled-molecule
@SQ SN:chr19 LN:59128983 am:19 ga:CM000681.1 sn:19 ra:NC_000019.9 un:chr19 AN:19,CM000681.1,NC_000019.9 sr:assembled-molecule
@SQ SN:chr20 LN:63025520 am:20 ga:CM000682.1 sn:20 ra:NC_000020.10 un:chr20 AN:20,CM000682.1,NC_000020.10 sr:assembled-molecule
@SQ SN:chr21 LN:48129895 am:21 ga:CM000683.1 sn:21 ra:NC_000021.8 un:chr21 AN:21,CM000683.1,NC_000021.8 sr:assembled-molecule
@SQ SN:chr22 LN:51304566 am:22 ga:CM000684.1 sn:22 ra:NC_000022.10 un:chr22 AN:22,CM000684.1,NC_000022.10 sr:assembled-molecule
@SQ SN:chrX LN:155270560 am:X ga:CM000685.1 sn:X ra:NC_000023.10 un:chrX AN:X,CM000685.1,NC_000023.10 sr:assembled-molecule
@SQ SN:chrY LN:59373566 am:Y ga:CM000686.1 sn:Y ra:NC_000024.9 un:chrY AN:Y,CM000686.1,NC_000024.9 sr:assembled-molecule
@SQ SN:chr1_gl000191_random LN:106433 am:1 ga:GL000191.1 sn:HSCHR1_RANDOM_CTG5 ra:NT_113878.1 un:chr1_gl000191_random AN:GL000191.1,NT_113878.1 sr:unlocalized-scaffold
@SQ SN:chr1_gl000192_random LN:547496 am:1 ga:GL000192.1 sn:HSCHR1_RANDOM_CTG12 ra:NT_167207.1 un:chr1_gl000192_random AN:GL000192.1,NT_167207.1 sr:unlocalized-scaffold
@SQ SN:chr4_gl000193_random LN:189789 am:4 ga:GL000193.1 sn:HSCHR4_RANDOM_CTG2 ra:NT_113885.1 un:chr4_gl000193_random AN:GL000193.1,NT_113885.1 sr:unlocalized-scaffold
@SQ SN:chr4_gl000194_random LN:191469 am:4 ga:GL000194.1 sn:HSCHR4_RANDOM_CTG3 ra:NT_113888.1 un:chr4_gl000194_random AN:GL000194.1,NT_113888.1 sr:unlocalized-scaffold
@SQ SN:chr7_gl000195_random LN:182896 am:7 ga:GL000195.1 sn:HSCHR7_RANDOM_CTG1 ra:NT_113901.1 un:chr7_gl000195_random AN:GL000195.1,NT_113901.1 sr:unlocalized-scaffold
@SQ SN:chr8_gl000196_random LN:38914 am:8 ga:GL000196.1 sn:HSCHR8_RANDOM_CTG1 ra:NT_113909.1 un:chr8_gl000196_random AN:GL000196.1,NT_113909.1 sr:unlocalized-scaffold
@SQ SN:chr8_gl000197_random LN:37175 am:8 ga:GL000197.1 sn:HSCHR8_RANDOM_CTG4 ra:NT_113907.1 un:chr8_gl000197_random AN:GL000197.1,NT_113907.1 sr:unlocalized-scaffold
@SQ SN:chr9_gl000198_random LN:90085 am:9 ga:GL000198.1 sn:HSCHR9_RANDOM_CTG1 ra:NT_113914.1 un:chr9_gl000198_random AN:GL000198.1,NT_113914.1 sr:unlocalized-scaffold
@SQ SN:chr9_gl000199_random LN:169874 am:9 ga:GL000199.1 sn:HSCHR9_RANDOM_CTG2 ra:NT_113916.2 un:chr9_gl000199_random AN:GL000199.1,NT_113916.2 sr:unlocalized-scaffold
@SQ SN:chr9_gl000200_random LN:187035 am:9 ga:GL000200.1 sn:HSCHR9_RANDOM_CTG4 ra:NT_113915.1 un:chr9_gl000200_random AN:GL000200.1,NT_113915.1 sr:unlocalized-scaffold
@SQ SN:chr9_gl000201_random LN:36148 am:9 ga:GL000201.1 sn:HSCHR9_RANDOM_CTG5 ra:NT_113911.1 un:chr9_gl000201_random AN:GL000201.1,NT_113911.1 sr:unlocalized-scaffold
@SQ SN:chr11_gl000202_random LN:40103 am:11 ga:GL000202.1 sn:HSCHR11_RANDOM_CTG2 ra:NT_113921.2 un:chr11_gl000202_random AN:GL000202.1,NT_113921.2 sr:unlocalized-scaffold
@SQ SN:chr17_gl000203_random LN:37498 am:17 ga:GL000203.1 sn:HSCHR17_RANDOM_CTG1 ra:NT_113941.1 un:chr17_gl000203_random AN:GL000203.1,NT_113941.1 sr:unlocalized-scaffold
@SQ SN:chr17_gl000204_random LN:81310 am:17 ga:GL000204.1 sn:HSCHR17_RANDOM_CTG2 ra:NT_113943.1 un:chr17_gl000204_random AN:GL000204.1,NT_113943.1 sr:unlocalized-scaffold
@SQ SN:chr17_gl000205_random LN:174588 am:17 ga:GL000205.1 sn:HSCHR17_RANDOM_CTG3 ra:NT_113930.1 un:chr17_gl000205_random AN:GL000205.1,NT_113930.1 sr:unlocalized-scaffold
@SQ SN:chr17_gl000206_random LN:41001 am:17 ga:GL000206.1 sn:HSCHR17_RANDOM_CTG4 ra:NT_113945.1 un:chr17_gl000206_random AN:GL000206.1,NT_113945.1 sr:unlocalized-scaffold
@SQ SN:chr18_gl000207_random LN:4262 am:18 ga:GL000207.1 sn:HSCHR18_RANDOM_CTG1 ra:NT_113947.1 un:chr18_gl000207_random AN:GL000207.1,NT_113947.1 sr:unlocalized-scaffold
@SQ SN:chr19_gl000208_random LN:92689 am:19 ga:GL000208.1 sn:HSCHR19_RANDOM_CTG1 ra:NT_113948.1 un:chr19_gl000208_random AN:GL000208.1,NT_113948.1 sr:unlocalized-scaffold
@SQ SN:chr19_gl000209_random LN:159169 am:19 ga:GL000209.1 sn:HSCHR19_RANDOM_CTG2 ra:NT_113949.1 un:chr19_gl000209_random AN:GL000209.1,NT_113949.1 sr:unlocalized-scaffold
@SQ SN:chr21_gl000210_random LN:27682 am:21 ga:GL000210.1 sn:HSCHR21_RANDOM_CTG9 ra:NT_113950.2 un:chr21_gl000210_random AN:GL000210.1,NT_113950.2 sr:unlocalized-scaffold
@SQ SN:chrUn_gl000211 LN:166566 am:na ga:GL000211.1 sn:HSCHRUN_RANDOM_CTG1 ra:NT_113961.1 un:chrUn_gl000211 AN:GL000211.1,NT_113961.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000212 LN:186858 am:na ga:GL000212.1 sn:HSCHRUN_RANDOM_CTG2 ra:NT_113923.1 un:chrUn_gl000212 AN:GL000212.1,NT_113923.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000213 LN:164239 am:na ga:GL000213.1 sn:HSCHRUN_RANDOM_CTG3 ra:NT_167208.1 un:chrUn_gl000213 AN:GL000213.1,NT_167208.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000214 LN:137718 am:na ga:GL000214.1 sn:HSCHRUN_RANDOM_CTG4 ra:NT_167209.1 un:chrUn_gl000214 AN:GL000214.1,NT_167209.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000215 LN:172545 am:na ga:GL000215.1 sn:HSCHRUN_RANDOM_CTG5 ra:NT_167210.1 un:chrUn_gl000215 AN:GL000215.1,NT_167210.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000216 LN:172294 am:na ga:GL000216.1 sn:HSCHRUN_RANDOM_CTG6 ra:NT_167211.1 un:chrUn_gl000216 AN:GL000216.1,NT_167211.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000217 LN:172149 am:na ga:GL000217.1 sn:HSCHRUN_RANDOM_CTG7 ra:NT_167212.1 un:chrUn_gl000217 AN:GL000217.1,NT_167212.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000218 LN:161147 am:na ga:GL000218.1 sn:HSCHRUN_RANDOM_CTG9 ra:NT_113889.1 un:chrUn_gl000218 AN:GL000218.1,NT_113889.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000219 LN:179198 am:na ga:GL000219.1 sn:HSCHRUN_RANDOM_CTG10 ra:NT_167213.1 un:chrUn_gl000219 AN:GL000219.1,NT_167213.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000220 LN:161802 am:na ga:GL000220.1 sn:HSCHRUN_RANDOM_CTG11 ra:NT_167214.1 un:chrUn_gl000220 AN:GL000220.1,NT_167214.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000221 LN:155397 am:na ga:GL000221.1 sn:HSCHRUN_RANDOM_CTG13 ra:NT_167215.1 un:chrUn_gl000221 AN:GL000221.1,NT_167215.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000222 LN:186861 am:na ga:GL000222.1 sn:HSCHRUN_RANDOM_CTG14 ra:NT_167216.1 un:chrUn_gl000222 AN:GL000222.1,NT_167216.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000223 LN:180455 am:na ga:GL000223.1 sn:HSCHRUN_RANDOM_CTG15 ra:NT_167217.1 un:chrUn_gl000223 AN:GL000223.1,NT_167217.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000224 LN:179693 am:na ga:GL000224.1 sn:HSCHRUN_RANDOM_CTG16 ra:NT_167218.1 un:chrUn_gl000224 AN:GL000224.1,NT_167218.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000225 LN:211173 am:na ga:GL000225.1 sn:HSCHRUN_RANDOM_CTG17 ra:NT_167219.1 un:chrUn_gl000225 AN:GL000225.1,NT_167219.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000226 LN:15008 am:na ga:GL000226.1 sn:HSCHRUN_RANDOM_CTG19 ra:NT_167220.1 un:chrUn_gl000226 AN:GL000226.1,NT_167220.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000227 LN:128374 am:na ga:GL000227.1 sn:HSCHRUN_RANDOM_CTG20 ra:NT_167221.1 un:chrUn_gl000227 AN:GL000227.1,NT_167221.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000228 LN:129120 am:na ga:GL000228.1 sn:HSCHRUN_RANDOM_CTG21 ra:NT_167222.1 un:chrUn_gl000228 AN:GL000228.1,NT_167222.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000229 LN:19913 am:na ga:GL000229.1 sn:HSCHRUN_RANDOM_CTG22 ra:NT_167223.1 un:chrUn_gl000229 AN:GL000229.1,NT_167223.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000230 LN:43691 am:na ga:GL000230.1 sn:HSCHRUN_RANDOM_CTG23 ra:NT_167224.1 un:chrUn_gl000230 AN:GL000230.1,NT_167224.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000231 LN:27386 am:na ga:GL000231.1 sn:HSCHRUN_RANDOM_CTG24 ra:NT_167225.1 un:chrUn_gl000231 AN:GL000231.1,NT_167225.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000232 LN:40652 am:na ga:GL000232.1 sn:HSCHRUN_RANDOM_CTG25 ra:NT_167226.1 un:chrUn_gl000232 AN:GL000232.1,NT_167226.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000233 LN:45941 am:na ga:GL000233.1 sn:HSCHRUN_RANDOM_CTG26 ra:NT_167227.1 un:chrUn_gl000233 AN:GL000233.1,NT_167227.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000234 LN:40531 am:na ga:GL000234.1 sn:HSCHRUN_RANDOM_CTG27 ra:NT_167228.1 un:chrUn_gl000234 AN:GL000234.1,NT_167228.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000235 LN:34474 am:na ga:GL000235.1 sn:HSCHRUN_RANDOM_CTG28 ra:NT_167229.1 un:chrUn_gl000235 AN:GL000235.1,NT_167229.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000236 LN:41934 am:na ga:GL000236.1 sn:HSCHRUN_RANDOM_CTG29 ra:NT_167230.1 un:chrUn_gl000236 AN:GL000236.1,NT_167230.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000237 LN:45867 am:na ga:GL000237.1 sn:HSCHRUN_RANDOM_CTG30 ra:NT_167231.1 un:chrUn_gl000237 AN:GL000237.1,NT_167231.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000238 LN:39939 am:na ga:GL000238.1 sn:HSCHRUN_RANDOM_CTG31 ra:NT_167232.1 un:chrUn_gl000238 AN:GL000238.1,NT_167232.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000239 LN:33824 am:na ga:GL000239.1 sn:HSCHRUN_RANDOM_CTG32 ra:NT_167233.1 un:chrUn_gl000239 AN:GL000239.1,NT_167233.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000240 LN:41933 am:na ga:GL000240.1 sn:HSCHRUN_RANDOM_CTG33 ra:NT_167234.1 un:chrUn_gl000240 AN:GL000240.1,NT_167234.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000241 LN:42152 am:na ga:GL000241.1 sn:HSCHRUN_RANDOM_CTG34 ra:NT_167235.1 un:chrUn_gl000241 AN:GL000241.1,NT_167235.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000242 LN:43523 am:na ga:GL000242.1 sn:HSCHRUN_RANDOM_CTG35 ra:NT_167236.1 un:chrUn_gl000242 AN:GL000242.1,NT_167236.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000243 LN:43341 am:na ga:GL000243.1 sn:HSCHRUN_RANDOM_CTG36 ra:NT_167237.1 un:chrUn_gl000243 AN:GL000243.1,NT_167237.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000244 LN:39929 am:na ga:GL000244.1 sn:HSCHRUN_RANDOM_CTG37 ra:NT_167238.1 un:chrUn_gl000244 AN:GL000244.1,NT_167238.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000245 LN:36651 am:na ga:GL000245.1 sn:HSCHRUN_RANDOM_CTG38 ra:NT_167239.1 un:chrUn_gl000245 AN:GL000245.1,NT_167239.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000246 LN:38154 am:na ga:GL000246.1 sn:HSCHRUN_RANDOM_CTG39 ra:NT_167240.1 un:chrUn_gl000246 AN:GL000246.1,NT_167240.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000247 LN:36422 am:na ga:GL000247.1 sn:HSCHRUN_RANDOM_CTG40 ra:NT_167241.1 un:chrUn_gl000247 AN:GL000247.1,NT_167241.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000248 LN:39786 am:na ga:GL000248.1 sn:HSCHRUN_RANDOM_CTG41 ra:NT_167242.1 un:chrUn_gl000248 AN:GL000248.1,NT_167242.1 sr:unplaced-scaffold
@SQ SN:chrUn_gl000249 LN:38502 am:na ga:GL000249.1 sn:HSCHRUN_RANDOM_CTG42 ra:NT_167243.1 un:chrUn_gl000249 AN:GL000249.1,NT_167243.1 sr:unplaced-scaffold
@SQ SN:chr6_apd_hap1 LN:4622290 am:6 ga:GL000250.1 sn:HSCHR6_MHC_APD_CTG1 ra:NT_167244.1 un:chr6_apd_hap1 AN:GL000250.1,NT_167244.1 sr:alt-scaffold
@SQ SN:chr6_cox_hap2 LN:4795371 am:6 ga:GL000251.1 sn:HSCHR6_MHC_COX_CTG1 ra:NT_113891.2 un:chr6_cox_hap2 AN:GL000251.1,NT_113891.2 sr:alt-scaffold
@SQ SN:chr6_dbb_hap3 LN:4610396 am:6 ga:GL000252.1 sn:HSCHR6_MHC_DBB_CTG1 ra:NT_167245.1 un:chr6_dbb_hap3 AN:GL000252.1,NT_167245.1 sr:alt-scaffold
@SQ SN:chr6_mann_hap4 LN:4683263 am:6 ga:GL000253.1 sn:HSCHR6_MHC_MANN_CTG1 ra:NT_167246.1 un:chr6_mann_hap4 AN:GL000253.1,NT_167246.1 sr:alt-scaffold
@SQ SN:chr6_mcf_hap5 LN:4833398 am:6 ga:GL000254.1 sn:HSCHR6_MHC_MCF_CTG1 ra:NT_167247.1 un:chr6_mcf_hap5 AN:GL000254.1,NT_167247.1 sr:alt-scaffold
@SQ SN:chr6_qbl_hap6 LN:4611984 am:6 ga:GL000255.1 sn:HSCHR6_MHC_QBL_CTG1 ra:NT_167248.1 un:chr6_qbl_hap6 AN:GL000255.1,NT_167248.1 sr:alt-scaffold
@SQ SN:chr6_ssto_hap7 LN:4928567 am:6 ga:GL000256.1 sn:HSCHR6_MHC_SSTO_CTG1 ra:NT_167249.1 un:chr6_ssto_hap7 AN:GL000256.1,NT_167249.1 sr:alt-scaffold
@SQ SN:chr4_ctg9_hap1 LN:590426 am:4 ga:GL000257.1 sn:HSCHR4_1_CTG9 ra:NT_167250.1 un:chr4_ctg9_hap1 AN:GL000257.1,NT_167250.1 sr:alt-scaffold
@SQ SN:chr17_ctg5_hap1 LN:1680828 am:17 ga:GL000258.1 sn:HSCHR17_1_CTG5 ra:NT_167251.1 un:chr17_ctg5_hap1 AN:GL000258.1,NT_167251.1 sr:alt-scaffold
Raw
michael_hoffmans_super_special_wishmaker.sh
wget -O - https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.13_GRCh37/GCF_000001405.13_GRCh37_assembly_report.txt \
| java -Xmx4g -jar fgbio-1.2.0-4798fd1-SNAPSHOT.jar \
CollectAlternateContigNames \
-i /dev/stdin \
-o michael_hoffmans_super_special_wishmaker.dict \
-p UcscName \
-a AssignedMolecule GenBankAccession RefSeqAccession
@nh13
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nh13 commented May 22, 2020

If you run the tool with --existing=/path/to/existing.dict, you can update an existing sequencing dictionary, which is useful if you want to retain contig ordering, or add in md5 checksums.

Run java -jar fgbio.jar ContigNames to get a list of tools that use this sequence dictionary (.dict):

...
'ContigNames' is not a valid sub-command. See fgbio --help for more information.
Did you mean one of these?
        UpdateIntervalListContigNames
        UpdateFastaContigNames
        UpdateGffContigNames
        UpdateDelimitedFileContigNames
        UpdateVcfContigNames

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