alignment_window
Read-only
Read one window of a BAM or SAM in this project: its reads, the depth across it, and what the pairs say about the library — the same window, filters and record cap the pileup draws. Wire reads into an alignment or a screen the way the pane's own hand-offs do.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| locus | No | the window, as a locus string (`ctgA:1-50,001`). Unset, it is the whole of the alignment's first reference — the window the panel opens on. | |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| min_mapq | No | hide reads below this mapping quality, as the pane’s Filter reads operation does. The reads are still counted — `hidden` says how many this removed. | |
| alignment | No | which BAM or SAM in this project, by name. Unset, it is the project's only alignment — and it refuses rather than guessing when there is more than one. | |
| max_reads | No | the record cap. More reads than this overlap the window and the result is an even SAMPLE of them, with `sampled` saying so — the pane’s own cap is the default. | |
| hide_secondary | No | drop secondary alignments (FLAG 0x100). | |
| hide_duplicates | No | drop reads marked as PCR or optical duplicates (FLAG 0x400). | |
| hide_supplementary | No | drop supplementary alignments (FLAG 0x800). |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| reads | Yes | the reads in the window after filters: name, reference, 1-based start and end, strand, MAPQ, CIGAR, TLEN and sequence — the shape an alignment or a screen takes | |
| hidden | Yes | reads in the window the filters removed — 0 with an active filter is a real answer | |
| window | Yes | the window actually read, as a locus string | |
| sampled | Yes | more reads overlap the window than the cap allows, so `reads` is an even sample rather than all of them | |
| coverage | Yes | the depth profile as bins across the window, in order | |
| depthPlot | Yes | the coverage track as the pileup draws it: each bin's lowest, mean and highest per-base depth over ALL reads, so a dropout narrower than a bin still shows in the minimum | |
| depth_max | Yes | the deepest bin | |
| depth_mean | Yes | mean depth across the window’s coverage bins, over ALL reads — the coverage track is full-depth, as BamView’s is, so filters do not move it | |
| read_count | Yes | how many reads that is | |
| insert_size | Yes | the |TLEN| band this library’s own proper pairs define — `min`, `max` and whether it was MEASURED here or is the untuned fallback, which is what decides whether an insert is abnormal |