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assemble_refbased -- do not fail when reads do not align #84

Merged
merged 7 commits into from
May 25, 2020
Merged

assemble_refbased -- do not fail when reads do not align #84

merged 7 commits into from
May 25, 2020

Commits on May 25, 2020

  1. fix assemble_refbased behavior to emit empty output instead of failin… 

    …g when no reads map to reference
    @dpark01
    dpark01 committed May 25, 2020
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  2. fix align_reads task to be robust to empty ref fasta input

    @dpark01
    dpark01 committed May 25, 2020
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  3. dont forget to samtools index the empty bam too

    @dpark01
    dpark01 committed May 25, 2020
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  4. force samtools index to emit .bai instead of .bam.bai

    @dpark01
    dpark01 committed May 25, 2020
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  5. samtools index both the all.bam and the mapped.bam when empty (the re… 

    …ad_utils.py does it for us when its non-empty
    @dpark01
    dpark01 committed May 25, 2020
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  6. add more author/email to workflow meta

    @dpark01
    dpark01 committed May 25, 2020
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  7. fix some python print statements

    @dpark01
    dpark01 committed May 25, 2020
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