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coverage's Introduction

coverage

This project aims to parse data from one of these two programs:

  • Mosdepth

      mosdepth --by ${intervals_bed} \
           --thresholds 5,10,20,30  \
           ${outut_prefix} ${bam}

  • GATK DiagnoseTagets

          java -jar /usr/gitc/GATK35.jar \
          -T DiagnoseTargets \
          -R ${ref_fasta} \
          -o ${output_name} \
          -I ${input_bam} \
          -L ${intervals} \
          -min ${minCov}

And organize it in a way that one could easily inspect how is the sequencing coverage in genes of interest.

Quickstart

Download and extract the proper release for your system, and then:

# For GATK DiagnoseTargets output
./coverage --vcf <coverage.vcf.gz> 1>stdout.tsv

# For Mosdepth '.thresholds.bed.gz' output
./coverage --bed <thresholds.bed.gz> 1>stdout.tsv

After that you'll have two files:

  • stdout.tsv
ENSG00000187634 SAMD11  Count: 15   Total Bases: 3246   Coverage 5x: 2831   10x: 2514   20x: 2252   30x: 2137
ENSG00000188976 NOC2L   Count: 19   Total Bases: 2250   Coverage 5x: 2250   10x: 2250   20x: 2250   30x: 2250
ENSG00000187961 KLHL17  Count: 12   Total Bases: 2134   Coverage 5x: 2071   10x: 2027   20x: 2012   30x: 1992
ENSG00000187583 PLEKHN1 Count: 15   Total Bases: 2327   Coverage 5x: 2327   10x: 2327   20x: 2316   30x: 2298
ENSG00000187642 PERM1   Count: 5    Total Bases: 2463   Coverage 5x: 2463   10x: 2463   20x: 2463   30x: 2447
...
  • *_coverage.json.gz
  "Identifier": "no_sample_id",
  "GitVersion": "",
  "GlobalTotalBases": 36726635,
  "GlobalCoveredBases5x": 36462766,
  "GlobalCoveredBases10x": 36290670,
  "GlobalCoveredBases20x": 35708523,
  "GlobalCoveredBases30x": 34512655,
  "PerGeneCoverage": {
    "ENSG00000000003": {
      "ENSG": "ENSG00000000003",
      "Symbol": "TSPAN6",
      "TotalBases": 753,
      "CoveredBases": 740,
      "BasesCovered5x": 753,
      "BasesCovered10x": 740,
      "BasesCovered20x": 722,
      "BasesCovered30x": 676
    },
    "ENSG00000000005": {
      "ENSG": "ENSG00000000005",
      "Symbol": "TNMD",
      "TotalBases": 954,
      "CoveredBases": 954,
      "BasesCovered5x": 954,
      "BasesCovered10x": 954,
      "BasesCovered20x": 954,
      "BasesCovered30x": 954
    },
    ...

coverage's People

Contributors

dschles avatar flaviaerius avatar igorcorrea avatar lmtani avatar

Watchers

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coverage's Issues

Add deployment configuration Issue

Hi @mendelics

facing the Issue while Add deployment configuration:

Error @sap/fiori:deploy-config cf --base ui5.yaml --config ui5-deploy.yaml

[2023-08-23 18:39:25] INFO get parameters
unexpected fault address 0x0
fatal error: fault
[signal SIGSEGV: segmentation violation code=0x80 addr=0x0 pc=0x45f79f]

goroutine 1 [running]:
runtime.throw({0x7f1c92?, 0x1?})
/usr/local/go/src/runtime/panic.go:992 +0x71 fp=0xc000139618 sp=0xc0001395e8 pc=0x433851
runtime.sigpanic()
/usr/local/go/src/runtime/signal_unix.go:825 +0x2ec fp=0xc000139668 sp=0xc000139618 pc=0x448c2c
aeshashbody()
/usr/local/go/src/runtime/asm_amd64.s:1343 +0x39f fp=0xc000139670 sp=0xc000139668 pc=0x45f79f
runtime.mapiternext(0xc000037880)
/usr/local/go/src/runtime/map.go:934 +0x2cb fp=0xc0001396e0 sp=0xc000139670 pc=0x40fa4b
runtime.mapiterinit(0x0?, 0xc000213540?, 0xc00018f791?)
/usr/local/go/src/runtime/map.go:861 +0x228 fp=0xc000139700 sp=0xc0001396e0 pc=0x40f728
reflect.mapiterinit(0x7aa2a0?, 0xc0001397b0?, 0xc0001397d0?)
/usr/local/go/src/runtime/map.go:1373 +0x19 fp=0xc000139728 sp=0xc000139700 pc=0x45ce59
github.com/modern-go/reflect2.(*UnsafeMapType).UnsafeIterate(...)
/home/circleci/go/src/github.com/SAP/cloud-mta/vendor/github.com/modern-go/reflect2/unsafe_map.go:112
github.com/json-iterator/go.(*mapEncoder).Encode(0xc000197830, 0xc00018f298, 0xc00007cd20)
/home/circleci/go/src/github.com/SAP/cloud-mta/vendor/github.com/json-iterator/go/reflect_map.go:257 +0x21c fp=0xc0001397e0 sp=0xc000139728 pc=0x67cdbc
github.com/json-iterator/go.(*OptionalEncoder).Encode(0xc0001188c0?, 0x0?, 0x0?)
/home/circleci/go/src/github.com/SAP/cloud-mta/vendor/github.com/json-iterator/go/reflect_optional.go:70 +0xa4 fp=0xc000139830 sp=0xc0001397e0 pc=0x6829c4
github.com/json-iterator/go.(*onePtrEncoder).Encode(0xc000213520, 0xc00018f298, 0xc0001976e0?)
/home/circleci/go/src/github.com/SAP/cloud-mta/vendor/github.com/json-iterator/go/reflect.go:219 +0x82 fp=0xc000139868 sp=0xc000139830 pc=0x675962
github.com/json-iterator/go.(*Stream).WriteVal(0xc00007cd20, {0x777e20, 0xc00018f298})
/home/circleci/go/src/github.com/SAP/cloud-mta/vendor/github.com/json-iterator/go/reflect.go:98 +0x158 fp=0xc0001398d8 sp=0xc000139868 pc=0x674c78
github.com/json-iterator/go.(*dynamicEncoder).Encode(0x79f100?, 0xc00018f601?, 0xc00007cd38?)
/home/circleci/go/src/github.com/SAP/cloud-mta/vendor/github.com/json-iterator/go/reflect_dynamic.go:15 +0x39 fp=0xc000139908 sp=0xc0001398d8 pc=0x677339
github.com/json-iterator/go.(*structFieldEncoder).Encode(0xc000197590, 0x76e9a4?, 0xc00007cd20)
/home/circleci/go/src/github.com/SAP/cloud-mta/vendor/github.com/json-iterator/go/reflect_struct_encoder.go:110 +0x56 fp=0xc000139980 sp=0xc000139908 pc=0x68adf6
github.com/json-iterator/go.(*structEncoder).Encode(0xc000197650, 0x8787c8?, 0xc00007cd20)
/home/circleci/go/src/github.com/SAP/cloud-mta/vendor/github.com/json-iterator/go/reflect_struct_encoder.go:158 +0x765 fp=0xc000139a68 sp=0xc000139980 pc=0x68b805
github.com/json-iterator/go.(*Stream).WriteVal(0xc00007cd20, {0x7b9aa0, 0xc000197140})
/home/circleci/go/src/github.com/SAP/cloud-mta/vendor/github.com/json-iterator/go/reflect.go:98 +0x158 fp=0xc000139ad8 sp=0xc000139a68 pc=0x674c78
github.com/json-iterator/go.(*frozenConfig).Marshal(0xc0001188c0, {0x7b9aa0, 0xc000197140})
/home/circleci/go/src/github.com/SAP/cloud-mta/vendor/github.com/json-iterator/go/config.go:299 +0xc9 fp=0xc000139b70 sp=0xc000139ad8 pc=0x66bda9
github.com/json-iterator/go.Marshal({0x7b9aa0?, 0xc000197140?})
/home/circleci/go/src/github.com/SAP/cloud-mta/vendor/github.com/json-iterator/go/adapter.go:34 +0x3b fp=0xc000139b98 sp=0xc000139b70 pc=0x6603fb
github.com/SAP/cloud-mta/mta.printResult({0x777e20?, 0xc00018f298?}, {0x0?, 0x1?, 0x0?}, 0x4000107?, {0x0?, 0x0?}, 0x816750, 0x816a20)
/home/circleci/go/src/github.com/SAP/cloud-mta/mta/mta_services.go:482 +0x2fe fp=0xc000139cd8 sp=0xc000139b98 pc=0x6ace5e
github.com/SAP/cloud-mta/mta.WriteResult(...)
/home/circleci/go/src/github.com/SAP/cloud-mta/mta/mta_services.go:467
github.com/SAP/cloud-mta/mta.RunAndWriteResultAndHash({0x7f50d5?, 0x533bf1?}, {0x7ffe5e530be6, 0x33}, {0x0?, 0x0, 0x0?}, 0x816820)
/home/circleci/go/src/github.com/SAP/cloud-mta/mta/mta_services.go:514 +0x14c fp=0xc000139d88 sp=0xc000139cd8 pc=0x6ad30c
github.com/SAP/cloud-mta/cmd.glob..func10(0xabcbc0?, {0xc00007a840?, 0x2?, 0x2?})
/home/circleci/go/src/github.com/SAP/cloud-mta/cmd/mta.go:220 +0x4f fp=0xc000139dd8 sp=0xc000139d88 pc=0x75810f
github.com/spf13/cobra.(*Command).execute(0xabcbc0, {0xc00007a800, 0x2, 0x2})
/home/circleci/go/src/github.com/SAP/cloud-mta/vendor/github.com/spf13/cobra/command.go:852 +0x67c fp=0xc000139eb0 sp=0xc000139dd8 pc=0x57f2bc
github.com/spf13/cobra.(*Command).ExecuteC(0xabe740)
/home/circleci/go/src/github.com/SAP/cloud-mta/vendor/github.com/spf13/cobra/command.go:960 +0x39c fp=0xc000139f68 sp=0xc000139eb0 pc=0x57f89c
github.com/spf13/cobra.(*Command).Execute(...)
/home/circleci/go/src/github.com/SAP/cloud-mta/vendor/github.com/spf13/cobra/command.go:897
github.com/SAP/cloud-mta/cmd.Execute(...)
/home/circleci/go/src/github.com/SAP/cloud-mta/cmd/root.go:33
main.main()
/home/circleci/go/src/github.com/SAP/cloud-mta/main.go:11 +0x25 fp=0xc000139f80 sp=0xc000139f68 pc=0x7596a5
runtime.main()
/usr/local/go/src/runtime/proc.go:250 +0x212 fp=0xc000139fe0 sp=0xc000139f80 pc=0x435f72
runtime.goexit()
/usr/local/go/src/runtime/asm_amd64.s:1571 +0x1 fp=0xc000139fe8 sp=0xc000139fe0 pc=0x462261
Do you need to install @sap/generator-fiori globally?
npm install -g @sap/generator-fiori
OR
yarn global add @sap/generator-fiori

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