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annotation.py — added get_bam_path(sample_id) helper; make_comparisons() now reads the bam_file column from samples.tab into bam_path_map; write_comparisons() and bam_count() use get_bam_path()
config/__init__.py — adds default bam_column = "bam_file"
__init__.py — initialises bam_path_map = {}
junctions.py, exons.py, genes.py, anchors.py — use annotation.get_bam_path(sample_id) instead of {bam_path}/{sample_id}.bam; exons/genes/anchors now iterate annotation.samples instead of scanning the directory
jbrowse2.py — write_sample_jobs() uses per-sample paths when bam_path_map is populated
How to use it — just add a bam_file column to samples.tab:
sample_id treatment_id bam_file
sample1 control data/samples/gregor@gmail.com/sample1/sample1.bam
sample2 test data/samples/gregor@gmail.com/sample2/sample2.bam
Existing samples.tab files without the column continue to work exactly as before using bam_path from splicekit.config.
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