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Added VIM to docker image (#134)
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* Added vim to docker container
* Updated Dockerfile to allow for new versions of packages.
* Added in samtools library dependencies for new pysam.
* Pinned pysam version.
* Fixed the `longbow correct` tests to work with padded data.
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@jonn-smith
jonn-smith authored Jun 27, 2022
1 parent 022f39a commit cdb191f
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Showing 5 changed files with 23 additions and 10 deletions.
10 changes: 7 additions & 3 deletions docker/Dockerfile
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Expand Up @@ -5,8 +5,9 @@ MAINTAINER Kiran V Garimella
ARG branch

# install gsutil
RUN apt-get update
RUN apt-get install -y curl git-lfs time datamash wget zlib1g-dev libssl-dev lbzip2 make gcc
RUN apt-get update --allow-releaseinfo-change
RUN apt-get update -m
RUN apt-get install -y curl git-lfs time datamash wget zlib1g-dev libssl-dev lbzip2 make gcc libbz2-dev libncurses5-dev libncursesw5-dev liblzma-dev
RUN curl https://sdk.cloud.google.com | bash

# Setup crcmodc for gsutil:
Expand Down Expand Up @@ -37,14 +38,17 @@ RUN wget https://github.com/samtools/samtools/releases/download/1.14/samtools-1.
&& tar xjf samtools-1.14.tar.bz2 \
&& rm samtools-1.14.tar.bz2 \
&& cd samtools-1.14 \
&& ./configure --without-curses --disable-lzma --disable-bz2 \
&& ./configure \
&& make \
&& make install

# install Starcode
RUN wget -O /usr/local/bin/starcode https://github.com/gui11aume/starcode/releases/download/1.4/starcode-1.4 \
&& chmod 755 /usr/local/bin/starcode

# Install vim so we can edit files later:
RUN apt-get install -y vim

# activate conda environment
ENV PATH="/longbow/venv/bin:/root/google-cloud-sdk/bin/:$PATH"
RUN echo "source /longbow/venv/bin/activate" >> ~/.bashrc
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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -24,7 +24,7 @@
'pandas',
'numpy',
'matplotlib',
'pysam>=0.16.0.1',
'pysam==0.19.1',
'progress',
'construct',
'pathos',
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3 changes: 3 additions & 0 deletions src/longbow/correct/command.py
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Expand Up @@ -487,6 +487,9 @@ def _correct_barcode_fn(in_queue, out_queue, bam_header_dict, barcode_tag, corre
read.set_tag(corrected_tag, new_bc)
read.set_tag(longbow.utils.constants.COULD_CORRECT_BARCODE_TAG, True)

print(f"Old BC: {old_bc}")
print(f"New BC: {new_bc}")

# Need to do some basic math for padded barcode strings:
if len(old_bc) > barcode_length:
end_pad_bases = int((len(old_bc) - barcode_length)/2)
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9 changes: 6 additions & 3 deletions tests/test_data/correct/correct_expected_corrected_data.sam
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Expand Up @@ -15,6 +15,9 @@ clr_barcode_in_whitelist 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d C
clr_barcode_lev_1_corrected 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:CCCCCCCCCCCCCCCT YC:i:1 YP:i:1 CB:Z:CCCCCCCCCCCCCCCC rq:f:-1 pz:i:0
clr_barcode_lev_2_corrected 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:CCCCCCCCCCCCCCTT YC:i:1 YP:i:1 CB:Z:CCCCCCCCCCCCCCCC rq:f:-1 pz:i:0
clr_barcode_lev_3_corrected 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:CCCCCCCCCCCCCTTT YC:i:1 YP:i:1 CB:Z:CCCCCCCCCCCCCCCC rq:f:-1 pz:i:0
ccs_multi_correction_success 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:AAAACCCCCCCCCCCCCCCCAAAA YC:i:1 YP:i:1 CB:Z:CCCCCCCCCCCCCCCC rq:f:1 pz:i:4
clr_multi_correction_success 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:AAAACCCCCCCCCCCCCCCCAAAA YC:i:1 YP:i:1 CB:Z:CCCCCCCCCCCCCCCC rq:f:-1 pz:i:4
ccs_multi_correction_same_barcode_success 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:CCCCCCCCCCCCCCCCCCCCAAAA YC:i:1 YP:i:1 CB:Z:CCCCCCCCCCCCCCCC rq:f:1 pz:i:0
ccs_multi_correction_success_no_change_1 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:AAAACCCCCCCCCCCCCCCCAAAA YC:i:1 YP:i:0 CB:Z:CCCCCCCCCCCCCCCC rq:f:1 pz:i:4
clr_multi_correction_success_no_change_2 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:AAAACCCCCCCCCCCCCCCCAAAA YC:i:1 YP:i:0 CB:Z:CCCCCCCCCCCCCCCC rq:f:-1 pz:i:4
ccs_multi_correction_success_change_1 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:AAAACCCCCCCACCCCCCCCAAAA YC:i:1 YP:i:1 CB:Z:CCCCCCCCCCCCCCCC rq:f:1 pz:i:4
clr_multi_correction_success_change_2 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:AAAACCCCCCCCACCCCCCCAAAA YC:i:1 YP:i:1 CB:Z:CCCCCCCCCCCCCCCC rq:f:-1 pz:i:4
ccs_multi_correction_same_barcode_success_1 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:CCCCCCCCCCCCCCCCCCCCAAAA YC:i:1 YP:i:0 CB:Z:CCCCCCCCCCCCCCCC rq:f:1 pz:i:0
ccs_multi_correction_same_barcode_success_2 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:CCCCCCCCCCCACCCCCCCCAAAA YC:i:1 YP:i:1 CB:Z:CCCCCCCCCCCCCCCC rq:f:1 pz:i:0
9 changes: 6 additions & 3 deletions tests/test_data/correct/correct_test_data.sam
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Expand Up @@ -22,8 +22,11 @@ clr_barcode_lev_3_corrected 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433
clr_barcode_lev_4_not_corrected 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:CCCCCCCCCCCCTTTT rq:f:-1
ccs_correction_equidistant 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:AGGGGGGGGTTTTTTC rq:f:1
clr_correction_equidistant 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:AGGGGGGGGTTTTTTC rq:f:-1
ccs_multi_correction_success 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:AAAACCCCCCCCCCCCCCCCAAAA rq:f:1
clr_multi_correction_success 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:AAAACCCCCCCCCCCCCCCCAAAA rq:f:-1
ccs_multi_correction_success_no_change_1 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:AAAACCCCCCCCCCCCCCCCAAAA rq:f:1
clr_multi_correction_success_no_change_2 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:AAAACCCCCCCCCCCCCCCCAAAA rq:f:-1
ccs_multi_correction_success_change_1 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:AAAACCCCCCCACCCCCCCCAAAA rq:f:1
clr_multi_correction_success_change_2 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:AAAACCCCCCCCACCCCCCCAAAA rq:f:-1
ccs_multi_correction_failure 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:GGGGGGGGGGGGGGGGGGGGGGGG rq:f:1
clr_multi_correction_failure 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:GGGGGGGGGGGGGGGGGGGGGGGG rq:f:-1
ccs_multi_correction_same_barcode_success 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:CCCCCCCCCCCCCCCCCCCCAAAA rq:f:1
ccs_multi_correction_same_barcode_success_1 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:CCCCCCCCCCCCCCCCCCCCAAAA rq:f:1
ccs_multi_correction_same_barcode_success_2 4 * 0 255 * * 0 0 GGGGGGGGGG ++++++++++ RG:Z:cd9b433d CR:Z:CCCCCCCCCCCACCCCCCCCAAAA rq:f:1

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