coral hsr command fails with TypeError: 'ChimericAlignment' object is not iterable #44
Description
Hi,
I'm running into an issue while trying to use the coral hsr command. When I execute it, I encounter the following error:
╭───────────────────── Traceback (most recent call last) ──────────────────────╮
│ /CoRAL/coral/cli.py:389 in hsr_mode │
│ │
│ 386 │ │ f"Performing HSR mode with options: {ctx.params}" │
│ 387 │ │ f"{colorama.Style.RESET_ALL}" │
│ 388 │ ) │
│ ❱ 389 │ hsr.locate_hsrs( │
│ 390 │ │ lr_bam, │
│ 391 │ │ cycles, │
│ 392 │ │ cn_seg, │
│ │
│ /CoRAL/coral/hsr.py:147 in locate_hsrs │
│ │
│ 144 │ │ rr_int = chimeric_alignments[r][1] │
│ 145 │ │ q_ = chimeric_alignments[r][2] │
│ 146 │ │ for interval in ecdna_intervals: │
│ ❱ 147 │ │ │ i = interval_overlap_l(interval, rr_int) │
│ 148 │ │ │ if i >= 0 and interval_include(rr_int[i], interval): │
│ 149 │ │ │ │ cycle_flag = True │
│ 150 │ │ │ │ break │
│ │
│ /CoRAL/coral/breakpoint/breakpoint_utilities.py:89 in interval_overlap_l │
│ │
│ 86 │ Check if an interval in the form of [chr, s, e] overlaps with any │
│ 87 │ a list of intervals. │
│ 88 │ """ │
│ ❱ 89 │ for other_intv_idx, other_intv in enumerate(other_intvs): │
│ 90 │ │ if intv.does_overlap(other_intv): │
│ 91 │ │ │ return other_intv_idx │
│ 92 │ return None │
╰──────────────────────────────────────────────────────────────────────────────╯
TypeError: 'ChimericAlignment' object is not iterable
Here’s how I’m calling the command:
coral hsr \
--lr-bam alignment.bam \
--cycles amplicon1_cycles.txt \
--cn-seg sample.call.cns \
--output-prefix sample \
--normal-cov 28.688
Any help would be appreciated.
Thanks!
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