metadata documenting how published data was prepared (ddb32220) · Commits · github_fork / Universc

test/shared/icell8-test/README.md

+2 −1

Original line number	Diff line number	Diff line
		@@ -11,7 +11,8 @@ Study Accession: EGAS00001002320
		https://ega-archive.org/studies/EGAS00001002320
		Data Accession: EGAD00001003443
		https://ega-archive.org/datasets/EGAD00001003443

		File Accession: EGAF00001698000
		Sample: 72618_KU812 (Human KU812 cells)

		## Data preparations
		Filtered for regions mapping to HUMAN_21:9825832-48085036 GRCh38 (hg38)

test/shared/icell8-test/README.temp.md

deleted100644 → 0

+0 −18

Original line number	Diff line number	Diff line
		/sequencedata/Hiseq2000/190408_D00364_0405_BHWLL2BCX2/Unaligned_for_Lane1/Project_LS3492_RNhi10764_Lane1/Sample_RNhi10764_190408_D00364_0405_BHWLL2BCX2/

		HiSeq2000 run on 2019/04/08 (1 lanes in rapid mode): Project_LS3492

		Tissue: MCF10A (breast cell line)

		Species: Homo sapiens (Human)

		Sample Provider: Shiori Aki (Umeda Lab, NAIST)

		Samples Prepared: Nicola Hetherington (RIKEN IMS)

		Single-cell (iCELL8)

		iCELL8 initiated:
		2019/01/24 (iCELL8_01)

		Note that UMI iCELL8 runs are being sequenced for comparison

test/shared/icell8-test/WellList_barcode.txt

0 → 100644

+1513 −0

Original line number	Diff line number	Diff line
		GTTGGATAGCC
		GTTGAGCTGCG
		CCTCCGCCTGC
		CCGTCCTCAGT
		TGGTACTATAT
		AAGAGAGACGC
		GGCTCGTTAGC
		ATTATATCTCA
		ATGGCCGTATG
		AAGAATTGCAT
		ATTCCGAGCGG
		AAGAATAACGA
		TCAATTACGAC
		CGGTTGGTAGA
		CCGTCCGTCGA
		CCAGACCAACC
		TTGGAGAGTAG
		CAATAGAATGG
		GGTCATAATGG
		TCAGAGCCTCG
		GTTATCGGACC
		GTTGGCGCGAC
		GGTATAGACTA
		AGAAGCCTTGG
		TTGATTCAGAT
		TGCGGTTCCTG
		ATTGCGTTCAA
		GCTTATGCTGC
		TTGAGAGTTCC
		CCTCCAACCGA
		GCTGCAACCTT
		ACGCAATCCTT
		TGCCTCTTCTG
		CGGTTGCCAGC
		CGAATCTAATT
		AACTCTAGTAT
		GGTTCAAGCAG
		CCATCTGAGAT
		ACTTCAGCGAT
		AGAACTATGGT
		CCGGTCATCTA
		GCAACCGCTCC
		CCTCTCTCATT
		TGGAGTATATT
		AACCTACGCGC
		ACGTACGGAAG
		GTCTGGTCCTT
		AACTTATTGCA
		GGTTCGTCTTG
		TGCTCTCTAGG
		AGAACCGCTTC
		CTATCAGCATC
		TGGTCCGCATC
		TAACCTCCGCG
		GGCGTCCGTTG
		TCGTATTCGCC
		GCTTGCCTTCG
		TTGGAACGTAA
		CTGGTTGCTGG
		CCTATCGTTGA
		AGAACCATAGG
		AAGAGAGAACG
		AACTAACCTTG
		TGGATGGCAGT
		TGGCCGAGCTG
		CCATAGCCTCA
		CCTCCGAGGAC
		AAGAACTAATC
		GGTATCTCTCG
		AGAATCAGTCT
		GGTTCCGTTGC
		AACGCTCCGGA
		AAGAGCAGAGC
		AGGTTAGTACG
		TGGATATTGCC
		TCGTTGCGTAC
		GCCAGCCGAAC
		TGCGGATGGTT
		GGCGGCTGCGA
		TAGCTAAGGCG
		CCTCTTACCTT
		GTTGGCAACGG
		GTAGGACCGAG
		CGTTAGATACC
		GGTTAAGTCTG
		AACTCATAGGA
		AAGACCGCCAT
		CAGCTTGGATT
		GCTTATGGAGT
		CGATGGTAATA
		TTCCTCGCATA
		GGTTACTCCTT
		GCTGGAGTAGG
		TAACCTTCCGG
		GAAGAGCGGTC
		AGAATCCGCAT
		TGCGGCATATC
		TTGATTAGCCA
		AACGCTGGATT
		AGGAACGATCA
		GGTACGGTACC
		GGTAACCTGAC
		CCTCGTATTCG
		CGCCAACTCGG
		TTGCTCTCAAG
		CCAATTGCTAG
		CCTCAGAACCG
		AACCAAGAACG
		ACCAGAACTCT
		CCAAGACTTCT
		GAAGCGCTTCC
		GTTCGGCGGAT
		CCGCATCGAGT
		TTGCTTACGGA
		AACCGCAAGAA
		CGTTGGCCTGA
		AGTCTGGCGCT
		GAACCTCGTCG
		GATTCTAGGTT
		TACGATCTACG
		GGCGTTGACTG
		TAGGTCGTCCT
		TGAGTTGCTCA
		AACTGAGAAGG
		GTTCAATTATG
		GAAGATTCCTT
		GTAAGCGCGCG
		ACCAGCTCTTG
		CTTGGATAACT
		ATTGATAGTCC
		GAACGGAGAGT
		TCAGGAACCTC
		TTCGTATACGT
		AGGTCGTACGC
		AGAAGTCATAG
		GTCTAACCTTA
		ACCATCGGATG
		GAATAAGTCAA
		CCAGGCCAGTC
		AACTGGTAGCA
		GTCTATGGCAA
		CCAGTTAGGTA
		GGTAGCCTTGC
		AGAACCGATAA
		CTCCTCCGTAG
		TGGTAACTGCT
		GCGAGCTGAAT
		AACCGCAACCT
		CTTCTTGACGG
		GTAACTTGGCA
		CCAGAAGATAG
		ACGAGACGGCT
		GGTAGTCTCCA
		TTCGGCTTGGA
		CCATTCCTTAC
		CGGCGCGGCGA
		GAACCGTCAGG
		CCGCCATGCCA
		CCTATTCATAT
		AACCTTGCAAG
		TTCTTACTTGC
		TCGGAGCAGAG
		TCTATACGATG
		GGTTGGTCATA
		CGTCTCAATTA
		TTGGTTGAATC
		AACGAGACGTC
		TGGCAGGATGC
		CAACCAGTTGC
		TGCGTAGGTAA
		ACGACCTAGGC
		CATCCGCTCAT
		CTCTATCTCAG
		AACGGATCAAT
		AACTCGCATGG
		GTCGCGAGTAA
		GAAGACGTCCT
		AAGAACGCCGG
		CGGATTGCTGA
		GTTCGTCGTTC
		AACCATCGTTC
		CGAACCGGATT
		CCGTCTGCGAA
		CGCCTCAGGAG
		TTGCTAGACCT
		CCTAAGTCCTC
		TTGGATCAGAA
		CCAACTCCGAT
		TGGCTGAGGCC
		CCTGGCCTTCA
		GTTGACCTCGG
		TCAATCAACCG
		TTCGCGCGTCA
		CGTTGCTGGAT
		CCGAACTGGAG
		AACGATAGCAT
		TTGATATACTA
		TGAGGTTGGCT
		CCTAACTAATT
		TGCTGGTTGGA
		CCTCGGTCTAT
		ATATGCGTTAG
		GTCTGCAACGC
		ACCAACTCTCA
		GGTATCCGTCC
		AACCTTATCGG
		GAACGGACCTC
		TGCCGGCGCGC
		CCAGCATTCGC
		CCAATGCCGCA
		CCTCGCTCGTA
		AAGACTAAGCT
		CCTCAAGCTAG
		CCGTAACTATT
		TTGAGACGGAT
		GTTGAGTCAAC
		GGAGTTCGTCT
		GTATGATCTAC
		GGAGCGTTGGT
		CCAATATATTA
		GCAGAGCTCGA
		GTTGCATTCCT
		GGTAAGATCTC
		TGAGGTATCTC
		AACGTAATCGC
		ACGAATAATCT
		TTCAGGTAGGA
		CCGCAACTAGG
		TTGAATTAATA
		GATGAGAGTAA
		ATGCAGTAACG
		GTATGCCTCTG
		AACTACCGCGA
		GCTATTGACTG
		GGTTCTCAGCA
		TTGGCAGTCGC
		TTGATGGATCT
		AGAACCTGGAA
		CCAATGCTGGT
		TGGACTATACC
		GCGCCAGCCTG
		TATCTGGCTGG
		TCGTTCAATCC
		GTAATTGCTCT
		GTCGGTTCCAT
		GCTCCGCTTCG
		TGGCGTTATCT
		CCAGCGCCAGT
		CCTAGATAATA
		CCGCGCTCTTC
		GGTAAGTAATA
		ACCAAGATATG
		CAACTAACCGA
		ATCTTGGACCT
		CCAACTAGTCA
		CGGAGGCTGCC
		CCTGCCGATCG
		AAGAGATAAGT
		GCGGTATAAGC
		AACTGCCTTGC
		AGAAGTAACTG
		GTTCGGTTCTT
		CGCTTCTGCTC
		CCGAACTCTAC
		CGGAGTAACTA
		CTGGATACTGC
		CCATCAATTAG
		GTTGATCATAG
		AACGTCTCATA
		GTACTGGCGCC
		CCTCAGGAGAG
		TAACCATCGAT
		TGGTAGCTATA
		AGGCTTAGATA
		TCGTTGGTCCG
		GTATATCGAAC
		AACGGAACGTT
		CGCGCCGGATA
		TGAGGCCTTCA
		CGGTAGAGGAC
		CCGTTACCTCG
		GCTCGCCTGAC
		CGGTATCCTGC
		AACTTCCATTC
		GGTTGGTAACG
		TTATACGTATC
		GGAGGCGGAGA
		GGTATTCCTGG
		TATATCGGAGG
		AACGGAGATAG
		CGGCTGCGTCA
		GCTTGGATAGT
		GTAGCCGAGAA
		AACGACGGCAA
		GGATCTCTCAA
		CTAGCTCCTAT
		AACCTTGATGA
		AACCTCGGCTT
		AACGATCTCCA
		GACTTGCATAA
		CATGGTTGCTC
		CGTAGCAGTTA
		TGGATCGGTCT
		GAGTTCTAGGA
		ACCAAGCGAGA
		GTTATAATTCT
		GTATTGCCTGA
		ATGGAGATGGC
		GCGAACGCTGC
		AACTTGCTCTT
		CCAATTCGACC
		TTCAGCGGCGA
		TTGGCAGCTTG
		AACTCCAGCAA
		CGGTATCTTAA
		GCGGTTGATAA
		ACCTCTCTTGG
		AACGCGCGGTT
		AACGCAAGCGA
		AACCTAACTCA
		CCAAGCGCATG
		CTACGCGAGCA
		TGACTGAGGAA
		TCGACCAAGAG
		CTAGCTCAAGA
		GGATGGATACG
		GTTGATACGCG
		GTATCCTAATC
		AAGAGATCATG
		AACCGCAGCTG
		CCATAAGGATG
		GCGTTGGCCGC
		AACCTGAGGCA
		GCTGGCGGCGC
		CCGGTTGACGG
		CTCCATCTGCG
		CGATGATGAGC
		AAGAATCGGTT
		GTTATTCCATC
		ACCAACCAGAG
		TGGTTACTTCA
		CAGCAACTCTT
		CGAACCATCGA
		TTATGACGCAG
		GTATTATGCGT
		CCAAGCTAGGA
		AACTGGCTACT
		GTTGAATAGTA
		CCTCAGTTCAA
		TATTGATCCAA
		TGGATCTCCAG
		GTTGACTATAC
		CTCTAACTAGA
		CCAACCTATTG
		TGGTTCGGAAG
		GTTAAGTTCGC
		AAGAGAAGAAT
		CTGGATTCCTT
		AGAACTGACCA
		GTTGGCTAGAA
		CGTAGGTTGAC
		GATTAGATTCT
		CCTCTAAGGAG
		GTAGTTCTGCC
		CGTTGATTGGC
		AACTGCCGGAT
		TCATGGCGCGA
		TTCTTAAGTAT
		AACGCAGAAGC
		AGAACTAGCAG
		TTCGCCAGGCC
		CCATATGGCGC
		CAACCTAACGG
		AACTTACGGAG
		TTGCCTGATGA
		CGAACCGAGAG
		GGCTGGTAGGT
		GAACTTGGTTG
		CGACCATCGAA
		CTCCAGCCTTC
		ACGAATACGCA
		AAGAACCGAAT
		CTCCTAACTTC
		AGAAGCGGAAC
		TGAACCAATTG
		TCAGTTCATAA
		AACGCGCAACG
		GCAGCCTCAAT
		CCAAGCTTGCC
		AACTAATTCAG
		TAACGAGCTCT
		CTAATCTTAAG
		GGATTGCAGTT
		TACGCTCTTCT
		GGTTCGACCAA
		GCGAACCGTCC
		TAGGCTACCTG
		AACTGGTCAGT
		CCTCTCTACTA
		CCATTCAATAG
		AACCGATATGA
		TTAGGACCAAC
		CTGGAGCTCTT
		CCATCTTACCT
		AACCAGCGCTG
		CAGCAATACTC
		GGTTGAGCATC
		TTATATCAGTT
		TGCAGTTCGCC
		ATTGACGCGCC
		GCATGGATTGG
		GCGGTCCATCC
		CCAGCGATAGC
		CCAGCTAATAG
		AAGAGATACCA
		ACGAGCTTCGC
		CAACCGCATCC
		TGCGATGATCA
		GGTTGGTATAT
		TGAGGCTGGAA
		GTTGCGCTTAT
		TCATCGCTTGA
		CTCCAGATCAG
		GATGGCTTAGA
		TCAACTACTAG
		AACGCCAGGCT
		GGTTAAGATCA
		TGATCTTCAGA
		GTCAAGTTCCT
		AACGAGTTGGA
		GTTCTTACTCC
		CTGCGAGCTGA
		GCCATTGGCAT
		TTGACTCCGTC
		GTCCTTGGTAG
		TGGATGAATTC
		AAGGAACCGAC
		CGGAGTCTTCA
		ACGAATTCCGG
		CTGGAGGTTAG
		TTGATAAGTAC
		TGGAGACTCTT
		TTGGCGCGCGG
		TCCTCCTTGCT
		ACGACGGTATT
		CGTTATATCAT
		GGTCGGCGAAC
		GCCAACCGTTG
		TATGATTCGGT
		CAAGAGATATG
		GCTGGTTGGCC
		CCAATCCATAA
		AGAACGCTCGC
		GTTAGAACCGT
		TCCTCGCGACG
		GAAGGAACTGG
		TTGGCAGAAGA
		CGACCTTCATC
		GCTGCTGCAAC
		TATACTTGCGA
		AACTCAATGAG
		GGTCTGAACCG
		CTTGAGAAGGA
		TTGGCATGCCT
		TGGCGACCGAA
		GAAGAGCCATT
		AAGAACCTAGC
		GGTCATATCCA
		TCAAGAGCTGC
		CCATCTGATGG
		TGGATACGGAC
		GGTCCGGACGA
		TTAGGTCCTTC
		GGATTGAGTCT
		AACTGCATCCG
		AATAACCAATT
		CGATAGGTTAG
		AAGAACTCGAG
		TCGGCTGGCGG
		TTGCCGCTGGA
		GAGTCGCGGCC
		TGAGTAGAAGA
		AAGACGCGACT
		TCCATGAAGGT
		ACGATACGGTA
		ATGATCGTTGG
		AAGAAGATCTC
		TCCTATAGTTC
		TCATACCGGCG
		TCAGCGTCGTC
		AGAAGTTGCCG
		GGTCGGCATTA
		GAACTGGCAAT
		ACTCAGTAACC
		GTATGAGGAGA
		CTTCCATTGGT
		AAGATAACGAC
		AACGGCTCGGT
		AACTCAGCCAA
		ATTCTCTCCTG
		TGGTAGATGGT
		GTCCTCGCCTG
		TGGTCTAGCGG
		TGAGTCTATAT
		TGACGATAGCT
		CGCGAGAGATA
		AGAAGACGGTT
		CGGAGGCTTGG
		TTATCGAAGAA
		ACCAGCCAGTT
		GTTCTCGCTGC
		CCGACTTCTAT
		CCTACGAGGCA
		TTCTCGGCTAA
		AGAAGATAATC
		CGTATTCGAGA
		AGAACGGCTAT
		TCAAGATTAAC
		AACTACGCTTA
		TTACCTTCTAA
		GGTTGAGAGAC
		ACCAAGAGCTC
		GTAGCTTGCTC
		GAAGCCGCAGT
		TGCTGCTATCC
		AAGAGAAGCGA
		ATTAGGCGGAG
		AGAACGCAAGG
		AGAATATCTAT
		GTTCCATATTC
		GTTATGAGCGT
		GGCTACGTAAG
		AACGCTTGCCA
		ACGACGAAGCG
		GTTCAACGGTT
		GCAACCATAGC
		AGAACTGCCTT
		GGTTATGGCGG
		CTGATCCAACG
		GTTACGTATCG
		TCGGAGGTACT
		TGGAAGGTTGG
		GGTTGGAATCA
		TGATTCGGCCT
		GAACGATCCGT
		GTATCTACTAC
		GAACCATCGCG
		TTGCCAGCGGA
		TTAGTACGTAC
		GATTCTCGCCA
		GGTAACTGGTT
		TCGTTATTACC
		CAGTTGGTAAT
		TGGAGCGGACG
		CGTTGGAACGT
		CTCCGGCAGGA
		AGAACCAGCGC
		TTGCTCGAGAG
		AACTCTAGCGC
		TTATCAGCTCG
		TGACGTTCAGG
		CGACCGACTAG
		AAGACGTTAAT
		GCTTGGAGAAC
		GCGGCTTATGC
		GTTCCTCAGGT
		CGATTGCTGGC
		GGTACCAACCT
		CTGCCTTCCGA
		AACGAAGCTCG
		GTTATCATCAA
		AACTGCCGCTC
		ACCATATTGAA
		TCCGTCTGGAG
		AACGCTCGCGT
		AGTTAAGTCGA
		AACTCGGAACT
		AAGAGAACCAG
		TCAACGCTCTT
		CGGCTGGCGCG
		CCAATGCTTAG
		GTTAGTCTCGT
		GTACTTGGATC
		AAGAATCCATC
		AACCATAACGT
		GTTCCGGCGAA
		TCGGCTGCTGA
		ATATAGTACCT
		GGAGTTGGCGA
		AACCTAAGCCG
		AACGCATCCGT
		CTCCGCGTCGT
		GGTTGCGTCTA
		AACTCATTCGC
		CTTATATGCGC
		GGTTATCTCGA
		TCGAGCGCTTG
		AACGTCATCAA
		CCAATCATCAA
		GGTAGAGAACC
		TGATAGCTCTG
		CCGGTCTACGA
		AAGAGCGTAAT
		TGGACTTACGC
		GAGTTGCCGTA
		CTGAGGCGTAA
		AACCGGAAGTT
		GCTGCTGAGGA
		TAACCTAATGC
		CGTCTCGTAGG
		AGAACTGAGAT
		CCAGGAACGTT
		TTGAAGCCGGA
		AAGAGCCGCGT
		CCGGCTCGACC
		GTAGTCAACTT
		TCGTTACGGAA
		TGATTGGACCG
		CAGCAGAATTA
		GACCAGGCCGA
		CGTCTTAAGCG
		AACTGCAGGCA
		AACTACCTTAA
		CCAGTCATTCT
		AACCGCTCATT
		CGGTCTGGAGC
		TGGAAGGCCAG
		AACGTCGCTAG
		TGGCAGTAGAC
		TGGAGACGATG
		AGAAGAAGACT
		AAGAACGATAG
		AAGAACCTCAG
		TTGAACCAGTC
		GGTTATCGTAG
		TTGGTAAGGAG
		AACTAGGACCG
		CGTCTATACCG
		TGGAATTCTTA
		AAGAAGAAGAT
		TCGGTCGAGCC
		GGATCGCGCCA
		ACTTCTCAAGA
		CGCAGAGAGCA
		AACCAACGCAA
		AACTCAGACTT
		TGGAAGATATC
		GAATAACTACC
		GAACGATGGCC
		TGCCTGACTTA
		AGAAGCCTCCA
		GCGTTAGACTC
		ATTGATATCTA
		ATTAAGATGAA
		ACCAACGAGCC
		CCTGAAGTCAA
		TGGCGGCGGAC
		AACGTAATATA
		TATTGGCCAGC
		GCGGACGTTGA
		CTTGCCTCTAC
		GGTACCGGTAA
		TGCAGTTCAGA
		GAGAAGGCTCT
		GTTGAATAAGG
		CAAGAACCTGA
		CTTCGCGTATA
		AAGAGCGGCCG
		GAACCTCAGGA
		TTCGGTCATAT
		CCAGCTAGCGG
		TGGATTCTATA
		TGAATATGGTA
		TGACTGCTTCA
		GTTAGGAGGCC
		TGGCATTGCAT
		GTTCAGCGCCT
		AAGAGATTGGA
		AAGCAACGAGT
		GTACGCAGCTC
		GTCCAATGCGC
		AACGTCCGGAC
		AACCATCTATT
		TGGCCTGGCCA
		AACCTATCTTG
		CCGGCTGGATT
		AACGCAACTGC
		AGAATAGGATT
		TCGAGAGAATG
		TTGAGGTTCTA
		CCAACGAAGTT
		GTAGAGATATC
		CTCCGACCTAG
		CTGGTTGGAAT
		CCAGAACCATT
		AACCGTCTCTA
		TCTATGATTCC
		GGTCCGCGCTG
		TGCTGGTCTTC
		AACCGAAGAAG
		AAGAATGCGAT
		CGTTAGATCGG
		GTCGTCATGCC
		GCGTTAAGTAA
		GTCGATAATTA
		GCTGCTATGAT
		TGAGGTCGATC
		TGGTACGCGAC
		AGAAGGTACCT
		AACGAATCGAG
		GTCGGTATGCA
		CCGTAATAAGC
		GCTTGCGAGCC
		GGATTGCTAGA
		ATCTTCAGCTA
		CCGGTATGATT
		AAGAATAGACG
		GTCTGAATCTC
		CAGTTATACGA
		GCGTTGCAGCC
		AGACCAAGCGT
		TCCGCAGCGAA
		GTTACCTGGAT
		GTTCGCTTAGG
		CAGGTAAGAGG
		CTAACCATTCA
		GCCTCTTACCA
		TTACGTCCAGC
		GGTATGAGCTG
		CCAGCAAGGTC
		TTGATCGCGCA
		TATTGGTACTC
		TCCTTCCATGC
		AACGACTGGAT
		GCGTTCTGCTA
		AGGTTCTATAA
		TCAACCTGCGC
		CGGAGAGGACC
		CCAACCGATAC
		GGTTGCCGGCC
		TGAGCTACGAG
		GGTCTAACTTA
		GAACCTGACCG
		TGGCCTATGCG
		AACTTATACGG
		CCTCCGAAGGA
		CAACCGAGTCT
		TGAGCTCATAC
		TCCAATCGAGT
		CTGCGATCTTG
		AACGGAGTATC
		ATTGGAGAGAT
		TAACGCATTAT
		GCAGATACCTC
		TTGCTGAGACT
		AAGAGATAGTC
		AAGAGCATGAC
		AACCAGGTCTA
		TAACGAAGGTC
		TCATCGTCCAA
		AACGAGCGGCC
		CGTTATGAACT
		CCTGCATCGTA
		AAGCAAGATCA
		TTGCATTGAAC
		TTCAAGAGGTT
		AACCTATAGTA
		AATATACTCTG
		TTAGTCGTATG
		GTAGTAAGGCC
		CCAGCCGGAGC
		GTTCTGCTCCA
		GTAAGGATATA
		TCGTTACCAAG
		AACCGCGCAGG
		TATATCTGCCG
		CGACTTAATAG
		AGAACCGAACC
		CGTTGCATGCA
		CTCCGAACGTA
		CCTCTCGTCTT
		TTCTACGCAGC
		CCGACGAACTA
		GCTCTCATTCT
		AACGGAATAGG
		TTCGCTGATTA
		CGGCGTCCTGA
		AACGTTAGGCC
		AACGTTACTCG
		GGTATAGATAC
		TTCATCTCTCG
		AACGACTACGG
		AGGTCCGTTGA
		AACCGCCATAT
		TTGGAGGCGCG
		GTTACTCTACT
		AACTAGCGGTA
		TGGTCGATCTC
		CCGTCCATCCT
		ACGCGCTGGAG
		TGGCGTCAATT
		CTAATTCCTTA
		TCTATCGCGCG
		CGGTAGAACCG
		GCCTCGCCGGT
		CGCCATAGGAT
		CTGGAGACGTC
		AACGGCCTTCG
		ATAACCAGACC
		AACGCGCCAGT
		CTGGCGGCATA
		CTTCGGAATAA
		GAAGCTGGCTG
		ACCATACTGGT
		CTTGGCCTGGT
		AACGTATAGGT
		CTCTTGGTAGC
		TAGTTACGATG
		TAGTTGCTAGC
		GTTGCAGTATT
		CCAGACCGAAG
		GAACGAGAATG
		AGGTTAATATT
		CCAACCAGGCC
		CGTCGCTGCTG
		GTTGGCAATTA
		CGTTCGGCCGC
		GTTAATGCAAC
		AGAAGTCAGGC
		CCATTATTCGG
		CCAATTGATGC
		CAGCGCAATCG
		CCATCGACTAT
		GTTACGACGAT
		GCCTATTATCG
		CCATGACTCTA
		GAACCTCGCTT
		CCTATCATGCG
		CTCCTCCGCCA
		ATTCCGGAGGT
		CGTAGGTAGTT
		CCGCTTGCGCT
		CCAGCTCTCCA
		AGAACGTTGAT
		CTTGCTAACCG
		TTAGGTACCTG
		GCATTCTAACC
		GCTTAGGTAAC
		GGATGGAGAGA
		GCTTGGACGTA
		GTTGGTAGCCT
		AACTTACCGTT
		ACCAGATGCAA
		CAGAACGAGCT
		CATTCTTCCAA
		TGCCTATTAGC
		GTTATATTGCG
		GTTCGAGAGCG
		ACTCCATCAAT
		AACGTAGATCT
		GTTCTACTTCC
		AAGAGAATTAA
		GGATAATCCGT
		GTTCTCTAGCA
		GAAGAGACTTG
		GGATATGGTTC
		TCCTCCATGGC
		CCAAGCGGTCC
		GCTGATGCCTG
		TTAGTCATACC
		AACGGATCCTG
		GGTATGGTCTT
		GGTTACTCTAG
		AACTTGACTCT
		AGCGTTCTCGA
		CGATATACGGT
		GAAGATAGGCT
		CTTGAGTAGAT
		AAGACTACTGA
		AACCGAGGTTG
		TTGGCCAGCTA
		TTGCAAGACTA
		CGACTCCTTGG
		GACTCGCTCAT
		ATTGCCGAAGA
		AGTAGGCGCTC
		TTGGTCGTTCC
		CTGGTAGTATA
		AGAACGCCGAG
		CCAGACTAAGG
		GTCGTTACTAG
		TGAATTAATCC
		TCAGATTAAGT
		CGGTCTTCTTC
		GGTCAGCCGCT
		TGGAGTTATAA
		AACGCCTGCTT
		AACGCCGCGCC
		CGGTTCAACTT
		AACGATCTTGG
		AACTGGAGAGA
		AGAGAACGACG
		CTTAGTATGGT
		AACGACCTGGC
		CCATCTAACTA
		CTTGGATCGAA
		GCAAGTATCCG
		ACCTCCGCCGG
		CGGATGCGTAC
		CCGCAAGCGCA
		TGGTATGCAGC
		CCGAATTAGCG
		GCTCCAGCTTC
		GTTACTTACCT
		GATTCTTCTGG
		CTCCAGGCAAG
		TTCCTCAATAT
		TGATATTGCTC
		AGGTTCCTTGG
		TGAGGACGCTA
		GCCAGTAGGCG
		TCAGATCCGTA
		GGTTGCCGTTG
		GGTAGACGCAT
		CCTTCTATTCT
		CAACCAATCCT
		CTCGACTGATA
		TTACGTTCCGT
		TCAACCTCGGT
		GAGTCGCTCTG
		ATTGCTGCTAC
		GCGCTTAGCTT
		GTAGTTGATGA
		CGTCCGGTTGC
		CCAACCAAGAA
		TGCTATCGATA
		GTAGAATAGAG
		GAAGCGAAGAA
		ATTGGTATTCG
		TGAGTACGAGC
		GCTCATCAAGT
		CCTCGCTGCAA
		AGAGAACCGCT
		CGTTACGCATG
		AGAAGGCTAGA
		CGGTATATCGA
		GTCTGGTATTC
		TCCTTCATAAT
		TTATTCTGGCT
		AGAAGCCAACG
		TCCTAACTCAT
		GCTGCTTGATT
		GTTGGCGAAGC
		AGAAGAAGCTC
		TGAGTCTAAGC
		CTAGGTTCTCA
		CGGCAGTTGCG
		GTAGAGTATAT
		CGATTGAGGTA
		GCTGCAGTCGA
		TTATCATATAA
		ATTGATGATTC
		CTTGCGTCCTT
		CTCCAGTTCTC
		TCAACTCAGGC
		CCATACGAGAA
		CAACCAATAGA
		GATTGACGTCC
		TTACTTAGATT
		TCCTGGCTGGT
		GAAGCAGACGC
		GAACCTGCGCT
		CCGCATTCCTG
		TGCGAGCATAA
		TTGGACTGGTC
		TATATAGTCTT
		CCATGGTACCG
		CGGCGGTAAGT
		TCAAGGCGGCA
		AACGCGCGCAA
		CTGGCCAGGTC
		TGGTAATAGAA
		TGGTCCGAGAG
		GGCCTCGACCA
		CGGTAGTTATG
		AACCATCCGAT
		AGAACTTCATA
		AACCAGAACCA
		GGCGGTCTACT
		TGATGGAGACC
		CTCCAACGCCG
		CGGATATCGAA
		AGAACCAACCG
		AAGACTCAGGA
		GATGAATTGAG
		GTTGGATTATA
		GAACCTGGACC
		AACTCAAGAGG
		AACTAGAGCCT
		CGTCTGCTGAC
		AACGCGACTTG
		GTTCGTCATGG
		GGACGGCGACG
		CCGCTTAGACG
		AGAAGACTCGT
		ATATTGCTCGA
		GAACCTACCGT
		TGGCGTACTGC
		AGTTACGGCAA
		CGGATGGTACC
		CTGGCTTGGAC
		CTGGTCGTCAT
		AGAAGGCAGAT
		TTCTCTTGCCG
		AACTCCAACGG
		GAGCAGAGTTG
		CAACCAGGCAG
		AACTTAATCTG
		CGTTGCATTGC
		CGGCTTATGGC
		CGAACTAACGT
		TGCGGTCGCGT
		AACTCGATGGC
		GAACCTAATCT
		AACTTAAGTAA
		ACGAACTGACG
		AACGACGCCGC
		TGCTCAGGCTG
		CTCCAGACTGA
		CCAATATGCAA
		TTGCTAATGAA
		TGGATTCGCTG
		GTCGTCTACGC
		GTAGTCTATTA
		ATTGGTTAATG
		AACGATGCGAC
		AGGTCGTTGAA
		CAGAATCTCGT
		GAACCGCAGCG
		TTAGGAGTATA
		GCTGCGGCTTG
		ATTAACTGGTC
		TGATTGCCTTC
		AACCTTGCCGT
		CTCTACGATTA
		AGAGAACCTTA
		AACGCATAACT
		TTGGTCGCCTC
		GGTACGTTCTA
		TTCCATGGTAA
		GAAGAGATGAG
		GCGTATGCGGA
		CTTCATATTAC
		CGCCAATTATA
		GTTCATTGGTC
		GCTCTTCCGTT
		CCTGACTTACT
		GAAGCGGACCT
		CGCCTATAATC
		CGACTAGATTG
		GGTTGGCTACC
		GAACGCTAAGG
		CAGAACGTAGA
		CCATCTGCAGC
		AACTGCAATTA
		AACTATAAGAG
		AACGGTCGTAA
		GGTTAGGACCG
		AGTTGCGCTAA
		GGTCTCGATCG
		CTCCGATCGGT
		TTGGTCCTACT
		CTTCATCGGCC
		CTTGCCTTCAT
		TGGTTGACCAT
		GATCTGCTAAC
		TTATATTAGCC
		CGTTCGATAGA
		CTTGATATGAA
		AGAATCTATGA
		CGCCAACCTCG
		ACCGAACCGAT
		AACCAGTCAGG
		CGAAGCCATCC
		GAACGGTACGC
		GAACCGCGAAC
		CCATGCAACGT
		AGAAGCCGTAA
		CGAAGGTAAGG
		CCAGTACGATA
		GTTGCGCAAGT
		CCGTCATTGCG
		GGTCTCAAGGT
		GCTTGGTCCAA
		TTACGCTCGTA
		CGTTATCTAGG
		TTGGAATATAG
		AACGCATGATG
		GGCTGGATGAT
		GCGTCTGAGTA
		GTAGGCGTATC
		AGAATAGCTCC
		TGGATCGGAGA
		AGAAGAGATTA
		ATTGATTGAAT
		GTAGTTAATCT
		GAACGGTTATT
		CCTCGAGAGGA
		CCGTTCGAAGC
		CTCGTTATACT
		TTCTCTATCCA
		CTGGCTGCGAG
		ACGTACGTCCG
		AAGAGAGCAGA
		AACGACGAAGA
		GTATCTGCTTA
		TTAGGTAGAAC
		CGATTCTAGAT
		TGCCTTCATCA
		GCCGATACTGC
		TGCGTAGTCGG
		AGAACGGAGGC
		GTTATTACTTG
		GGCTGAACGTA
		CGTTGATAATC
		AACGAATCTTA
		CTTCCGCTCGC
		TCCTGAGCTCG
		GTTGCCTCAGG
		GCTCGGTTCCA
		TCGCGAAGGTT
		AGTCGGTCATG
		CCTCTCCATGA
		GGTAGGAGGTA
		GAGTTGACCAA
		GTTACGATTGC
		CCTTCGATTGC
		ACTTCGCAGGT
		TATGATATTGC
		CCGCCAAGTTC
		AACGAGAGATT
		TGGAGGTTGCG
		GCATCAAGATC
		AGTTGCGCGCG
		AAGACTATCAT
		AAGAGAATATC
		AAGGAACCTGG
		CTTGCGGATCT
		AACGGTCAAGT
		GTCTTCAGTCA
		TTGGCCATTCG
		CTGGCGCATTA
		AACGATTAGGC
		AGACCAACGGC
		GGCTCATGCGC
		GTTCCGATCAA
		AACGGAATCCA
		CCAAGCATAAC
		CTCTTGCTACT
		TGGTCGAGGCA
		CAACCATACGA
		GGTAGCAACGC
		GGTTCTTATAC
		TAGCGTTCTTC
		GCTCCTCCTGG
		ACGCATGAGGC
		CCAACGTCTCT
		AACCTAAGTTC
		AACTCCGGCCT
		CTCTAAGGTCG
		ATAACCAGTAG
		TTCATGGAACG
		CCATTAGACTG
		CCTCTGATTAG
		CTACGTCTGCA
		AACTTATATAT
		TGGCGCCTAAT
		GTTCCGAGCTC
		TTCTGGATCGC
		AGAACCATTCC
		TCAATTAGTAT
		ACGACTCTGAT
		CGTCCGAAGAG
		GGTTATAAGCT
		GGTTGGCTTGG
		AACGCCTAGCG
		TCGTTCTTGGT
		CCGAGGATAGC
		GGTTCTGAATA
		CCGCGCATCAA
		TCTAGCATGGC
		TCCGGCTCTGA
		TCCAACTGACT
		CCATGAAGGAC
		AGAACGAATAG
		AGAATACTCTA
		CAAGCAGTACT
		CAACGCAGAAC
		CTCTCGCTGCC
		TTACGACCGCA
		TATTGCTAGGT
		GCATCCTGCCT
		AACCGCTCGAG
		CCTCGGAGCTA
		TTGAGCGCGTC
		AACGTTGCAGA
		TCCTTGGACGG
		CCTCGATACTG
		CGTAACCTCTT
		ACCAACGAAGG
		CTCCGAGGATC
		CCAACTGCTTA
		CCGCAGGCCGG
		GGCGTATAGAA
		GTATAATATCT
		GCTTCGTTCTT
		CAGGACGTCTG
		CTTCGGTTGCG
		GCAAGATAGGT
		AACTTCAGATG
		AGAAGCATTAT
		CTGGTTCATTC
		CCGAACGGAAC
		GCTATGGCAAC
		CCTTCCTGCGC
		GTTGAAGTTCG
		GTCTGCGTTCC
		TCGGTTGGAGT
		TCGTTAAGTTC
		GGATGGTACGG
		GCCGGTTGAAG
		TGGAAGACTCC
		AAGAGAACGCA
		GGTAGGCATCC
		CCAGATCCTAA
		AACCATATCAA
		ATTATTCAGGT
		CCGCGTCGGCG
		CCAAGCAACTG
		GAACCGGTCTA
		CTGGAAGCTCT
		TGGTTCGCTCG
		TTCCTATTCAA
		CCAATTCTTGA
		CCGTATGGAAT
		GGTCAACCATG
		TTGGTCATAGG
		GTTGAGACCGC
		CAGGCAATGAT
		TGCGTCGATGG
		CGTTGCGCCGT
		GACCAACTGCT
		CCATATTACTC
		GCAGTTGCCAG
		CTCTCCGACGG
		AACGCCATATG
		TATTCTAGGAA
		TGCGTAATAGA
		TGGTTAGATTG
		GAAGCGTCCTG
		GTTATCTTCCT
		CTCCTTCTCGC
		AACCGAAGGTA
		AGTCTCGGAAC
		TGCGATCGGAA
		CTGGATGGCAA
		GGTAAGGCATG
		TCGCCAGTTCC
		AGAACCTTGCG
		ATGGTTGAGAG
		GCGCTGATTCA
		GGTCGGAGCGG
		GTAGAGGTTGG
		TGGTCATCCGG
		TTACTCGGCGC
		TTCGAATACTA
		AAGACCATACC
		TTGCATAACGT
		GTCGGCTGGAT
		TTGCCGAAGCG
		GTACGTTAAGT
		CCAAGATGCCG
		AACGCTCGACC
		CCTAATGCATG
		GGTTCGGATAA
		GTCTGGCGCGG
		GAACCGGCTCC
		AGAAGGATCGG
		CCATATAAGCG
		GAAGAGGCTGC
		AACTCATTATT
		TCGTTGCCGGA
		TTGCTCAACGC
		TGAGGCTTCGC
		GAACGGACTCG
		GTCGGTCAACG
		AACTATAATGA
		CGCAGCTTAGA
		GTTCGCGGTCC
		TGAGTACTTAA
		TTGATGCGGAA
		AAGAGATATAG
		CGACTTATCTT
		AAGAGCAGTTA
		ACCAACCATGC
		AGAAGAGCATG
		GGTAGCTAATT
		CCGAATATACG
		AGAATCCAGAG
		CTGGTACGTCT
		TAGTAGGATTA
		GGTTAGATGGC
		AACCGCATTAG
		GTCTTATGGTA
		GAACCTTATAG
		GGTAATTGATC
		CCTCTCAGCTG
		GGTAGTCAGAC
		AAGAGGCTAGT
		GGCTTGGCGAT
		CCAGCTCTGGC
		CCATCGCATAC
		TGGATCCTCAT
		AAGACTCCAGG
		GGTTCATCAAG
		AGTATTATAGA
		CCATAAGAGTT
		GAGTTATTAGT
		AATAACCATCC
		GGTAGCTGACC
		AACGCAGTAAG
		CCATCGTTAAC
		AACGGCATGCC
		GTCTTGGCATG
		CTGGCATGATA
		CCAATGGACTC
		ACCAATAGCAA
		AACTATACGCA
		TTCGGATAATG
		TTGAGATGAAC
		AACTCGTAGTC
		CCTCATCAGCG
		TATGGCTCTTA
		GCCGCCTACGG
		CTATGACCTAA
		GCTGCGTCCTC
		CAAGCGCGCAG
		GTCCGCGACGG
		TTGGAACGGTT
		AGAATCATCAG
		TTACTGCTTAC
		ATTCGCGCGAA
		GGTAGCTTCGT
		GTTAGCTATGA
		TGATCCTCAAT
		GTTCATTATAA
		CGTCAAGTCCA
		TGGAATATTAA
		CCTCCTGGACT
		GCCTGAACCAA
		AACCTTAGTAG
		CTGCGTACGGT
		CGCATCTGCAT
		AACCTGGCTCC
		TGATTATGAGA
		TTCTTAGCGAG
		AACCTCATACG
		CGAACCAGTCG
		GAACCAATATC
		CGCGCGCAGCC
		CCAAGCATTCG
		GAAGCCTTCCG
		TTAATCTCGAG
		CCATACCGCCT
		CTGGAGCAACC
		GCCGCTTGCTG
		TCAGGTTATCG
		GGTCGCCGCAA
		CGGTTCATGGT
		TCCTTAGAATT
		TTCTTATCCGC
		GCTGGCTCTAA
		CGACTGCCAAG
		GAACTACTAGT
		CCGCCTCAGTC
		GAACCTCCGAC
		CCAACTCTCTC
		AACCAGACTTA
		AACTTGAACGT
		CCTTATCCTCG
		CCAGCCTCCGG
		TTGAAGGTCTC
		ATTCCGAGTCC
		GGAACCGCCTA
		AACCGGACGGA
		CAACCAGAGAA
		AACCAGGCGGC
		AAGACGATATG
		CCAACGATCCT
		GATTCGTTAGA
		GACTCAAGCCT
		CCTATCTCGAA
		TTCCATTAAGG
		CCAACGCAAGC
		AACGAAGCGGA
		AAGAATAGGAA
		TGGCAGACTAA
		AACCATACCTC
		GTTGCGTTATC
		CCAGCTCCATA
		TTGCGTATGCA
		GGAGGCATTGA
		AACCTCGAACT
		CCATGGACGTC
		AAGACTTCCAA
		TTGCGTATCTG
		TTATTGGAGAT
		CTCTACCGTTC
		GCTGATGCGCC
		AACGAGGAGAG
		TTATACGAGGC
		TGAGTCCGTTA
		CCAATCTCCGC
		TTGAAGCTAGG
		GCGTCGGTTCT
		CTTAGGACGCA
		GAACGACTGCG
		TGCTTGATAGC
		GTTAGACGCCA
		GCTGCTCATAT
		AACGATCAGTT
		CCAATAGATCG
		TGAGGATAGTA
		CCAACTGAGCC
		CCTCCTCTGCA
		AACTACGGTCC
		CTTGATGACCA
		TGGCGGAGCAT
		CTCCGCTTAAG
		CTTGCGCTGCT
		AGAACTGCAGC
		CAACCGTACCG
		CCAGCATGAAG
		TAGTATCTTGA
		CAACGAATTAA
		GTATATACCGT
		TCGATCTCTGG
		CTCGGTAGAGA
		ACCAATTACTA
		TAGTCAGCCTC
		GTTGCCAGTAG
		CTTGACTCGGT
		TTCTCCTGGTA
		TGGTTCCTAAC
		AGAATATACGT
		CCAACCTCAAG
		CAACCAGATCG
		GCATTCATCAG
		GCCGTCGCGCT
		CTCTGGTTCCT
		CCTTAATACTT
		AACGACGATAC
		AAGAATCATTG
		GCTGGTCTACC
		CGGTTATAGCA
		GGTCATCATCT
		GATTCCGTCCT
		GTCCTTGATCA
		GAACTACCGTT
		TCAATCCATTC
		CTATGGTCGTA
		CCGTTCCATGG
		GTATACCAGAT
		CGTTAGTTCTA
		GGTTGAAGATA
		TCCTTCGAGAT
		AAGAACGCAAC
		CCGACCTTAAT
		AACTCGCTCGA
		TTGGCTACCAA
		CTTGATCAGGC
		TGGCTCCGCGA
		GGCGTCGTCAT
		GTAGTCGTCCA
		CAATCCATAGT
		GTTAGTTCCTG
		AACCGAATACT
		GTCCATCGCTC
		CCATCTCAATC
		CTGGCTGGTTG
		TGGATAGACGG
		GGTCTGCTCGC
		GAGGTTAGTTG
		GAACTCGAATT
		GTTGCGATCGT
		TGGCTATGCCG
		AACGGAGACGT
		CCAAGTAACCT
		CCAGAATCAGC
		GGTATTCAGCG
		GCAATACCGCT
		CCTCTTGCTCG
		CGAAGACCGGT
		GTATTCGCGAC
		AACTTCTAACG
		ACCAATGCGAG
		AACTATAGGTC
		GAGAACTGCCG
		CCTACTATGAC
		CCATCAACTGC
		TTGATACCAGC
		ATATTGGCTAA
		CCAAGAAGACC

test/shared/icell8-test/prepare_files.sh

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test/shared/icell8-test/update_sam_file_indels.R

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Original line number	Diff line number	Diff line
		args = commandArgs(trailingOnly=TRUE)
		print(args)
		sam_file <- data.table::fread(as.character(args[1]), data.table = F, skip = 3, header = F, fill=TRUE)
		vcf_file <- data.table::fread(as.character(args[2]), data.table = F, skip = 28, fill = TRUE)

		head(sam_file)
		head(vcf_file)

		sam_temp <- sam_file[,12:19]

		if(nrow(vcf_file) > 0 ){
		# reverse order by position to avoid upstream indesl affecting target position
		for(ii in c(nrow(vcf_file)):1){
		print(paste("replace", vcf_file[ii,5], "with", vcf_file[ii,4], "at chr", vcf_file[ii,1], "pos", vcf_file[ii,2]))
		vcf_pos <- vcf_file[ii,2]
		vcf_chr <- vcf_file[ii,1]
		vcf_ref <- vcf_file[ii,4]
		vcf_alt <- vcf_file[ii,5]
		ref_len <- nchar(vcf_file[ii,4])
		alt_len <- nchar(vcf_file[ii,5])
		sam_pos <- sam_file[,4]
		sam_chr <- sam_file[,3]
		sam_seq <- sam_file[,10]
		sam_qual <- sam_file[,11]
		#print(head(sam_file[,10]))
		read_length <- sapply(sam_file[,10], nchar)
		#print(head(read_length))
		#print(head((sam_chr == vcf_chr)))
		#loci <- apply(sam_file, 1, function(read) c(as.numeric(read[4]):as.numeric(read[4])+nchar(read[10])))
		# print(head( sam_pos ))
		# print(head( sam_pos+read_length ))
		# print(head( vcf_pos ))
		# print(head( (vcf_pos <= sam_pos) & (vcf_pos >= sam_pos+read_length) ))
		# print(table( (vcf_pos >= sam_pos) & (vcf_pos <= sam_pos+read_length) ))
		matched_reads <- ((sam_chr == vcf_chr) & (vcf_pos >= sam_pos) & (vcf_pos <= sam_pos+read_length))

		# print(which(matched_reads))
		# print(table(matched_reads))
		# print(sam_seq[matched_reads])
		# print(sam_qual[matched_reads])



		print(vcf_pos)
		print(alt_len)
		print(ref_len)
		# print(sam_pos[matched_reads])
		# print(sam_pos[matched_reads] + read_length[matched_reads])
		# print(vcf_pos - sam_pos[matched_reads] + 1)
		# print( substr(sam_seq[matched_reads], vcf_pos - sam_pos[matched_reads] + 1, vcf_pos - sam_pos[matched_reads] + alt_len) )
		# print(sam_seq[matched_reads][vcf_pos - sam_pos[matched_reads] + 1])
		print( substr(sam_seq[matched_reads], vcf_pos - sam_pos[matched_reads] + 1 -1, vcf_pos - sam_pos[matched_reads] + alt_len + 1) )
		print ( vcf_ref )
		#substr(sam_seq[matched_reads], vcf_pos - sam_pos[matched_reads] + 1, vcf_pos - sam_pos[matched_reads] + alt_len) <- vcf_ref
		for(jj in c(1:length(sam_seq))[matched_reads]){
		sam_seq[jj] <- paste(c(substr(sam_seq[jj], 0, vcf_pos - sam_pos[jj]),
		vcf_ref,
		substr(sam_seq[jj], vcf_pos - sam_pos[jj] + alt_len + 1, nchar(sam_seq[jj]))),
		collapse = "")
		sam_qual[jj] <- paste(c(substr(sam_qual[jj], 0, vcf_pos - sam_pos[jj]),
		vcf_ref,
		substr(sam_qual[jj], vcf_pos - sam_pos[jj] + alt_len + 1, nchar(sam_qual[jj]))),
		collapse = "")
		}
		print( substr(sam_seq[matched_reads], vcf_pos - sam_pos[matched_reads] + 1 -1, vcf_pos - sam_pos[matched_reads] + ref_len + 1) )
		# print(sam_seq[matched_reads][vcf_pos - sam_pos[matched_reads] + 1])
		#substr(sam_qual[matched_reads], vcf_pos - sam_pos[matched_reads] + 1, vcf_pos - sam_pos[matched_reads] + alt_len) <- paste0(rep("I", ref_len), collapse = "")
		# print( substr(sam_seq[matched_reads], vcf_pos - sam_pos[matched_reads] + ref_len, vcf_pos - sam_pos[matched_reads] + ref_len ) )
		sam_file[,10] <- sam_seq
		sam_file[,11] <- sam_qual
		}

		#update CIGAR
		read_length <- sapply(sam_file[,10], nchar)
		sam_file[,6] <- paste0(read_length, "M")

		sam_file[,10] <- sam_seq
		sam_file[,11] <- sam_qual

		sam_file[sam_file == ""] <- NA
		}
		#print(sam_file[23,])
		#print(sam_file[24,])
		sam_file <- sam_file[,1:19]
		sam_file[,12:19] <- sam_temp

		out_name <- paste0(c(as.character(args[1]), ".converted.sam"), collapse = "")
		out_name <- gsub(".sam.converted" ,".converted", out_name)
		print(out_name)
		write.table(sam_file, file = out_name, col.names = FALSE, quote = FALSE, row.names = FALSE, sep = "\t", na = "NA")

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