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Replaced SAM example

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Current one from https://genome.sph.umich.edu/wiki/SAM. Readable by the "VladaMilch/pdProbeRemap" package.
This commit is contained in:
Waldir Leoncio 2021-09-03 12:05:56 +02:00
parent 800bd33376
commit 15f2cbcf08
3 changed files with 1892 additions and 6 deletions
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2
R/greedyMix.R
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@ -14,7 +14,7 @@ greedyMix <- function(data, format, verbose = TRUE) {
} else if (format == "sam") {
stop("SAM files not yet supported." )
# TODO #18: implement load_sam()
} else if(format == "genepop") {
} else if (format == "genepop") {
# TODO #19: implement load_genepop()
stop("GenePop files not yet supported." )
} else {

1879
inst/ext/example_drosophila.Aligned.out.sam Normal file
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File diff suppressed because it is too large Load diff

17
inst/ext/sam_example.sam
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@ -1,5 +1,12 @@
HWI-ST865:416:C6CG0ACXX:1:1313:9073:43827 0 I 2 1 99M * 0 0 CCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCT @C@DFDEFFHDFFIIJIGIIGIGGIIIIJGHGIJJEEIAHHGGIGFH@HGCFGGGJJIIGDAFG@DGIHHHHHFFBB@CACEC6;?CDD?CDCAD>>AA AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:99 YT:Z:UU
HWI-ST865:416:C6CG0ACXX:1:1215:16359:6484 16 I 9 1 85M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCC EEEEFFFFDAGHHHIJJIIJJJJJIJJJJIJIJJIGIIJJJJJJJIJJJJJJJIIJJJIIJGJJIJJJJJJJHFHHHFFFFFCCB AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:85 YT:Z:UU
HWI-ST865:416:C6CG0ACXX:1:1113:14118:89232 16 I 15 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA CAC@A>C@AADCAC@ACEEC@@BD?E;@CEHGCEIGIHAFHGGF;FCHBHFBHIGIIIJJJJJJJJJJJJJJJJJJJJJIJJJJJJJHHHHHFFFFFCCC AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100 YT:Z:UU
HWI-ST865:412:C6CLLACXX:1:2315:12173:84819 16 I 49 1 70M * 0 0 GCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCT @7)3CC=)CA;EBC>DAEDBDCDDDCDD@B?<DEDE399CBC<+>EAE<BDCEAE3DADDD<ABDD;1?? AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:70 YT:Z:UU HWI-ST865:412:C6CLLACXX:1:1201:19323:33842 16 I 71 0 100M * 0 0 AAGCCTAAGCCTAAGCCTAAGCCTAAGCCAAATCCCAAGCCTAAGCCTAAGCCTAAGCCTAAGCCAGAGCCTAAGCCTAAGCCTTAGCCTAAGCCTGATC DDDCCDCCACCCDCCCC>CAA@D@;BDHA3A7(@5/IIHFIIGEIIIIHEIIIIIGGIGIIIIIFDCIIIIIIIIGGIIGIHFFEIHDDBHFFDDDB@@@ AS:i:-33 XS:i:-33 XN:i:0 XM:i:8 XO:i:0 XG:i:0 NM:i:8 MD:Z:29T2G2T29T0A17A11A1G1 YT:Z:UU
HWI-ST865:412:C6CLLACXX:1:1215:19021:78287 16 I 93 1 66M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGC @=87=3GF=.:CFE;D@B3?3?BD9BC<>CJJJJJJJJJJJJJJJJIJJJJJIHHHHHFFEDAC@B AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:66 YT:Z:UU
@HD VN:1.0 SO:coordinate
@SQ SN:1 LN:249250621 AS:NCBI37 UR:file:/data/local/ref/GATK/human_g1k_v37.fasta M5:1b22b98cdeb4a9304cb5d48026a85128
@SQ SN:2 LN:243199373 AS:NCBI37 UR:file:/data/local/ref/GATK/human_g1k_v37.fasta M5:a0d9851da00400dec1098a9255ac712e
@SQ SN:3 LN:198022430 AS:NCBI37 UR:file:/data/local/ref/GATK/human_g1k_v37.fasta M5:fdfd811849cc2fadebc929bb925902e5
@RG ID:UM0098:1 PL:ILLUMINA PU:HWUSI-EAS1707-615LHAAXX-L001 LB:80 DT:2010-05-05T20:00:00-0400 SM:SD37743 CN:UMCORE
@RG ID:UM0098:2 PL:ILLUMINA PU:HWUSI-EAS1707-615LHAAXX-L002 LB:80 DT:2010-05-05T20:00:00-0400 SM:SD37743 CN:UMCORE
@PG ID:bwa VN:0.5.4
@PG ID:GATK TableRecalibration VN:1.0.3471 CL:Covariates=[ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate, TileCovariate], default_read_group=null, default_platform=null, force_read_group=null, force_platform=null, solid_recal_mode=SET_Q_ZERO, window_size_nqs=5, homopolymer_nback=7, exception_if_no_tile=false, ignore_nocall_colorspace=false, pQ=5, maxQ=40, smoothing=1
1:497:R:-272+13M17D24M 113 1 497 37 37M 15 100338662 0 CGGGTCTGACCTGAGGAGAACTGTGCTCCGCCTTCAG 0;==-==9;>>>>>=>>>>>>>>>>>=>>>>>>>>>> XT:A:U NM:i:0 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:37
19:20389:F:275+18M2D19M 99 1 17644 0 37M = 17919 314 TATGACTGCTAATAATACCTACACATGTTAGAACCAT >>>>>>>>>>>>>>>>>>>><<>>><<>>4::>>:<9 RG:Z:UM0098:1 XT:A:R NM:i:0 SM:i:0 AM:i:0 X0:i:4 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:37
19:20389:F:275+18M2D19M 147 1 17919 0 18M2D19M = 17644 -314 GTAGTACCAACTGTAAGTCCTTATCTTCATACTTTGT ;44999;499<8<8<<<8<<><<<<><7<;<<<>><< XT:A:R NM:i:2 SM:i:0 AM:i:0 X0:i:4 X1:i:0 XM:i:0 XO:i:1 XG:i:2 MD:Z:18^CA19
9:21597+10M2I25M:R:-209 83 1 21678 0 8M2I27M = 21469 -244 CACCACATCACATATACCAAGCCTGGCTGTGTCTTCT <;9<<5><<<<><<<>><<><>><9>><>>>9>>><> XT:A:R NM:i:2 SM:i:0 AM:i:0 X0:i:5 X1:i:0 XM:i:0 XO:i:1 XG:i:2 MD:Z:35