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AfshinLab / BLR

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Add version number to blr log files and to SAM headers. #22

Closed pontushojer closed 4 years ago

pontushojer commented 4 years ago

This PR adds the version tag to log files and to SAM headers. See below for examples.

Log files

$ cat tag_fastq.log 
SETTINGS FOR: tagfastq (version: 0.2.dev26+gde2c535)
 uncorrected_barcodes: barcodes.fasta.gz
 corrected_barcodes: barcodes.clstr
 input1: trimmed.fastq
 input2: None
 output1: trimmed.barcoded.1.fastq.gz
 output2: trimmed.barcoded.2.fastq.gz
 barcode_tag: BX
 sequence_tag: RX
 mapper: bowtie2
. . .

SAM header

$ samtools view -H mapped.sorted.tag.bam
@HD VN:1.0  SO:coordinate
@SQ SN:chrA LN:50000
@SQ SN:chrB LN:40000
@SQ SN:chrC LN:9000
@SQ SN:chrD LN:1000
@RG ID:1    SM:20   LB:blr  PU:unit1    PL:ILLUMINA
@PG PN:bowtie2  ID:bowtie2  VN:2.3.5.1  CL:"/Users/pontus.hojer/miniconda3/envs/blr/bin/bowtie2-align-s --wrapper basic-0 -p 4 --rg-id 1 --rg LB:blr --rg SM:20 --rg PU:unit1 --rg PL:ILLUMINA --reorder --maxins 2000 -x ../blr-testdata/ref.fasta -1 trimmed.barcoded.1.fastq.gz -2 trimmed.barcoded.2.fastq.gz"
@PG PN:blr  ID:tagbam   VN:0.2.dev26+gde2c535    CL:"/Users/pontus.hojer/miniconda3/envs/blr/bin/blr tagbam mapped.sorted.bam -o mapped.sorted.tag.bam"