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Follow up to PR #418 #430
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Follow up to PR #418 #430
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e09dc65
UPDATES TO THE Hifiasm pipeline:
SHuang-Broad d3afc4b
For both CCS/ONT, update PBSV
SHuang-Broad 3a2ac5c
For both CCS/ONT, update Sniffles-2
SHuang-Broad 29aa964
CRITICAL: updating pbindex to that from the SMRTLink 12 release
SHuang-Broad 0262525
MAJOR REFACTOR: UNIFY CCS/ONT WGS PIPELINE
SHuang-Broad 7be9309
MISC UPDATES TO SEVERAL UTILS TASKS
SHuang-Broad 1ff0912
New docker that's intended to replace lr-basic:
SHuang-Broad 4224ab4
New docker that offers a new mode remove duplicates from a queryname-…
SHuang-Broad a13a541
New docker that updates the samtools in GATK to the latest (1.18)
SHuang-Broad 2905c69
significantly boost capabilities of BAMutils.wdl
SHuang-Broad b16c619
update some legacy code due to new interfaces in updated BAMutils.wdl
SHuang-Broad c96ea8e
New workflows
SHuang-Broad 39d77d2
Improve various existing codes
SHuang-Broad cbfed4e
New workflow to save files (avoid multiple calls to Finalize)
SHuang-Broad 8039c88
New workflow to unify QC and metrics collection on aligned BAM
SHuang-Broad b16155f
Update grouping of pipelines in .dockstore.yml
SHuang-Broad 5bf0b2f
update WDL validation bash script
SHuang-Broad 0d61935
DEPRECATION
SHuang-Broad 989ead1
Fix bug in deduplicating aligned ONT BAM
SHuang-Broad b8e67ff
DEPRECATION:
SHuang-Broad e5a79c2
Update utility code:
SHuang-Broad b5dc978
a few tweaks to to AlignedBamQCandMetrics:
SHuang-Broad 1abcc7a
correct two mistakes: 1. a typo; 2. should append not replace
SHuang-Broad da5bfb0
make read-length util tasks pre-emptible
SHuang-Broad 7975d6d
make fingerprint reads extraction more efficient/resilient
SHuang-Broad 5620d74
fix a stupid logical typo error (in saving files)
SHuang-Broad e910bac
option to force run fingerprintcheck on small bams
SHuang-Broad 04b82f8
make pbindex task more frugal
SHuang-Broad 14be4e2
Safer and more efficient way to do targetted pileup conversion
SHuang-Broad 136091a
Update Pacbio alignment task
SHuang-Broad d95be34
New subworkflow to align PacBio uBAM
SHuang-Broad 1e26de7
Two new workflows:
SHuang-Broad 44b7330
bug fix for bam2fastq
SHuang-Broad 526765e
optimize alignment further
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,73 @@ | ||
| FROM python:3.9.16-slim-bullseye | ||
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| COPY remove_duplicate_ont_aln.py /opt/ | ||
| COPY remove_duplicate_ont_namesorted_unaligned.py /opt/ | ||
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| RUN pip install pysam==0.21.0 | ||
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| # install gcloud and gsutil cli | ||
| ARG DEBIAN_FRONTEND=noninteractive | ||
| RUN apt-get -qqy update --fix-missing && \ | ||
| apt-get -qqy dist-upgrade && \ | ||
| apt-get -qqy install --no-install-recommends \ | ||
| apt-transport-https \ | ||
| ca-certificates \ | ||
| gnupg \ | ||
| zlib1g-dev \ | ||
| curl \ | ||
| wget \ | ||
| tree \ | ||
| tabix && \ | ||
| echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] https://packages.cloud.google.com/apt cloud-sdk main" | tee -a /etc/apt/sources.list.d/google-cloud-sdk.list && \ | ||
| curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key --keyring /usr/share/keyrings/cloud.google.gpg add - && \ | ||
| apt-get -qqy update && \ | ||
| apt-get -qqy install --no-install-recommends google-cloud-cli && \ | ||
| gcloud config set core/disable_usage_reporting true && \ | ||
| gcloud config set component_manager/disable_update_check true && \ | ||
| gcloud config set metrics/environment github_docker_image && \ | ||
| apt-get -qqy purge gnupg && \ | ||
| apt-get -qqy clean && \ | ||
| rm -rf /tmp/* \ | ||
| /var/tmp/* \ | ||
| /var/cache/apt/* \ | ||
| /var/lib/apt/lists/* \ | ||
| /usr/share/man/?? \ | ||
| /usr/share/man/??_* | ||
|
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| # install latest samtools | ||
| ARG DEBIAN_FRONTEND=noninteractive | ||
| ARG SAMTOOLS_VERSION=1.18 | ||
| ARG BCFTOOLS_VERSION=1.18 | ||
| RUN apt-get -qqy update --fix-missing && \ | ||
| apt-get -qqy dist-upgrade && \ | ||
| apt-get -qqy install --no-install-recommends \ | ||
| ca-certificates \ | ||
| libbz2-dev \ | ||
| libcurl4-openssl-dev \ | ||
| liblzma-dev \ | ||
| libncurses5-dev \ | ||
| autoconf \ | ||
| automake \ | ||
| bzip2 \ | ||
| gcc \ | ||
| make \ | ||
| wget \ | ||
| zlib1g-dev && \ | ||
| wget https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 && \ | ||
| tar xjf samtools-${SAMTOOLS_VERSION}.tar.bz2 && \ | ||
| cd samtools-${SAMTOOLS_VERSION} && ./configure --without-curses --enable-libcurl && make -s all all-htslib && make install install-htslib && cd - && \ | ||
| rm -rf samtools-${SAMTOOLS_VERSION}* && \ | ||
| wget https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \ | ||
| tar xjf bcftools-${BCFTOOLS_VERSION}.tar.bz2 && \ | ||
| cd bcftools-${BCFTOOLS_VERSION} && ./configure --without-curses && make -s && make install && cd - && \ | ||
| rm -rf bcftools-${BCFTOOLS_VERSION}* && \ | ||
| apt-get -qqy purge autoconf automake bzip2 gcc make wget && \ | ||
| apt-get -qqy clean && \ | ||
| rm -rf /tmp/* \ | ||
| /var/tmp/* \ | ||
| /var/cache/apt/* \ | ||
| /var/lib/apt/lists/* \ | ||
| /usr/share/man/?? \ | ||
| /usr/share/man/??_* && \ | ||
| samtools --help && \ | ||
| bcftools --help |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| VERSION = 0.1.2 | ||
| TAG1 = us.gcr.io/broad-dsp-lrma/lr-bam-dedup:$(VERSION) | ||
| TAG2 = us.gcr.io/broad-dsp-lrma/lr-bam-dedup:latest | ||
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| all: build push | ||
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| build: | ||
| docker build -t $(TAG1) -t $(TAG2) . | ||
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| push: | ||
| docker push $(TAG1) | ||
| docker push $(TAG2) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,76 @@ | ||
| import argparse | ||
| import pysam | ||
|
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| def main(): | ||
| parser = argparse.ArgumentParser(description='Remove redundant alignment records from ONT BAM file', | ||
| prog='remove_redundant_reads') | ||
| parser.add_argument('-p', '--prefix', type=str, default="shard", help="Output prefix") | ||
| parser.add_argument('-a', '--annotations', type=str, help="Annotations on (potential) duplicate reads") | ||
|
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| parser.add_argument('bam', type=str, help="BAM") | ||
| args = parser.parse_args() | ||
|
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| # create a dict of set's, a trick to avoid Hash collisions | ||
| guilty_dict_per_chr = dict() | ||
| with open(args.annotations) as f: | ||
| for line in f: | ||
| arr = line.strip().split('\t') | ||
| name = arr[0] | ||
| chrom = arr[2] | ||
| guilty_dict_per_chr.setdefault(chrom, set()) | ||
| guilty_dict_per_chr[chrom].add(name) | ||
|
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| print("chromosomes on which there are duplicate records:") | ||
| print(f" {guilty_dict_per_chr}") | ||
|
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| # Silence message about the .bai file not being found. | ||
| pysam.set_verbosity(0) | ||
|
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| num_alignments, num_dropped_alignments = 0, 0 | ||
| duplicate_signatures = [] | ||
| bf = pysam.Samfile(args.bam, 'rb', check_sq=False) | ||
| with pysam.Samfile(f'{args.prefix}.bam', 'wb', header=bf.header) as out: | ||
| # we rely on the observation that for coordinate sorted BAM, | ||
| # duplicate records will appear in blocks, hence once we step off a position with duplicates, we start afresh | ||
| current_position = -1 | ||
| current_signatures = set() | ||
| for read in bf: | ||
| num_alignments += 1 | ||
|
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| chrom = read.reference_name | ||
| n = read.query_name | ||
| if chrom in guilty_dict_per_chr and n in guilty_dict_per_chr[chrom]: | ||
|
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| mq = read.mapping_quality | ||
| sam_flag = read.flag | ||
| pos = read.reference_start | ||
| cigar = read.cigarstring | ||
| signature = f"{n}-{chrom}-{pos}-{mq}-{sam_flag}-{cigar}" | ||
|
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| if current_position != pos: # new position, let's write and reset | ||
| out.write(read) | ||
| current_position = pos | ||
| current_signatures = set() | ||
| current_signatures.add(signature) | ||
| elif signature in current_signatures: # You're a duplicate record, and not appearing for the 1st time! | ||
| num_dropped_alignments += 1 | ||
| duplicate_signatures.append(signature) # same signature may appear more than twice, hence list and append | ||
| pass | ||
| else: # you are in a new group of duplicates that map to this location | ||
| out.write(read) | ||
| current_signatures.add(signature) | ||
| else: | ||
| out.write(read) | ||
|
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| print(f'num_alignments: {num_alignments}') | ||
| print(f'num_dropped_alignments: {num_dropped_alignments}') | ||
| print(f'num_kept_alignments: {num_alignments - num_dropped_alignments}') | ||
|
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| with open(f'{args.prefix}.duplicate.signatures.txt', 'w') as out: | ||
| for sig in duplicate_signatures: | ||
| out.write(f"{sig}\n") | ||
|
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||
|
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| if __name__ == "__main__": | ||
| main() |
48 changes: 48 additions & 0 deletions
48
docker/lr-bam-dedup/remove_duplicate_ont_namesorted_unaligned.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| import argparse | ||
| import pysam | ||
|
|
||
|
|
||
| def main(): | ||
| parser = argparse.ArgumentParser(description='Remove redundant reads from renamed-sorted ONT BAM file', | ||
| prog='remove_redundant_reads') | ||
| parser.add_argument('-p', '--prefix', type=str, default="shard", help="Output prefix") | ||
| parser.add_argument('-q', '--qnames', type=str, help="Read names of duplicate records") | ||
|
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| parser.add_argument('bam', type=str, help="BAM") | ||
| args = parser.parse_args() | ||
|
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| # Silence message about the .bai file not being found. | ||
| pysam.set_verbosity(0) | ||
| bf = pysam.Samfile(args.bam, 'rb', check_sq=False) | ||
|
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| num_records, num_dropped_records = 0, 0 | ||
| duplicate_record_names = list() | ||
|
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| with pysam.Samfile(f'{args.prefix}.bam', 'wb', header=bf.header) as out: | ||
|
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| # we rely on the observation that for queryname sorted, unaligned BAM, | ||
| # if two neighboring records have the same query name, then they must be duplicate of each other | ||
| current_qm = '' | ||
|
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| for read in bf: | ||
| num_records += 1 | ||
|
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| n = read.query_name | ||
| if n == current_qm: | ||
| duplicate_record_names.append(n) | ||
| num_dropped_records += 1 | ||
| else: | ||
| current_qm = n | ||
| out.write(read) | ||
|
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| print(f'num_records: {num_records}') | ||
| print(f'num_dropped_records: {num_dropped_records}') | ||
| print(f'num_kept_alignments: {num_records - num_dropped_records}') | ||
|
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| with open(args.qnames, 'w') as outf: | ||
| for qn in duplicate_record_names: | ||
| outf.write(f'{qn}\n') | ||
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|
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| if __name__ == "__main__": | ||
| main() |
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I haven't reviewed this. Going to assume it's OK.