v0.20.0

What's Changed

• Notebooks: ask again when a download's server fails (§18.10) by @js2264 in #154
• Documentation site (§32), its pictures, and the fixes writing it found by @js2264 in #157
• Docs: live examples, the app itself in place of its picture (§32.4) by @js2264 in #158
• Docs: a live view takes the page's width, the contents list stepping aside by @js2264 in #159
• Timings: a deep human map, start to finish (§18.10) by @js2264 in #161
• Label scaled metaplot axes by feature position, not column by @js2264 in #155
• Add cell-of-its-own rectangle to Contact maps card by @js2264 in #156
• Docs in PR previews; docs look like the app and a third shorter; embeds fill and resize their frame by @js2264 in #160
• Move viewer timings to a separate notebook by @js2264 in #162

Full Changelog: v0.19.0...v0.20.0

v0.19.0

What's Changed

• Add example sessions to landing page by @js2264 in #144
• Measure analyses in the app as well as on the command line by @js2264 in #145
• CI: hold the subsample and every normalisation to cooler and cooltools, run on the day by @js2264 in #147
• Signal by group: one value per entry by default by @js2264 in #148
• Compartments: divide by cooltools' own expectation by @js2264 in #146
• Add TAD annotation (Juicer's Arrowhead, ported) and the map report by @js2264 in #149
• Describe the site to AI agents in full: llms.txt and five reference pages (§11, §23) by @js2264 in #150
• Laptop notebook: run each analysis in the app in Chromium, Firefox and WebKit (§18.10) by @js2264 in #152
• Remove telemetry entirely (§1, §11, §13, §18.10; §31 removed) by @js2264 in #153
• Service worker: answer only the app's own address, so llms.txt and a 404 open as themselves (§11) by @js2264 in #151

Full Changelog: v0.18.0...v0.19.0

v0.18.0

What's Changed

• Domain pileup over expected: rescaled local window by @js2264 in #141
• Speed up base composition and P(s) calculation by 8× and 2.5× by @js2264 in #142
• Base composition on indexed FASTA; TSV/bedGraph in pieces by @js2264 in #143

Full Changelog: v0.17.0...v0.18.0

v0.17.0

What's Changed

• Validate cis and trans, the saddle, FRiP and signal by group; signal by group reads exactly (§18.8, §18.10) by @js2264 in #125
• Add parity notebook comparing app and CLI outputs by @js2264 in #126
• Add laptop.qmd: benchmark 23 analyses on your own machine by @js2264 in #127
• Peak calling 9.6× faster genome-wide in under a quarter of the memory, results bit-identical by @js2264 in #128
• Test .hic reader against Juicer Tools demo file with hic-straw by @js2264 in #129
• Notebooks: references get a process a core, renders log the memory, timings weigh every process by @js2264 in #130
• pastis-NB fit runs on multiple threads with reproducible results by @js2264 in #131
• Add Notebooks tab to About dialog with task reference citations by @js2264 in #132
• Add anonymous telemetry and allow-access button for remembered files by @js2264 in #135
• Telemetry: honour Global Privacy Control, not Do Not Track; shorter About blurb by @js2264 in #136
• The lower triangle in a reading of its own (§5.10) by @js2264 in #137
• Add Fig. 1a and Fig. 2 to the paper's store, and § 24 to the validation notebook by @js2264 in #138
• Pairs stats: pairtools stats on import, the Pairs statistics card, and Pairs QC with restriction fragments (§3.7, §18.8) by @js2264 in #134
• Paper store: GM12878's second CTCF track is UW's (ENCFF644EEX) by @js2264 in #139
• Jupyter and R widgets: the viewer in a notebook cell, R Markdown, Quarto and Shiny (§21.5) by @js2264 in #133
• Validation § 24: name its peaks' columns itself, not with § 5's key by @js2264 in #140

Full Changelog: v0.16.0...v0.17.0

v0.16.0

What's Changed

• The page says when a picture is finished, and at what resolution (§12, §21.4) by @js2264 in #115
• Publish to npm by trusted publishing, without a token by @js2264 in #116
• A file let go on any cell of the deck lands there; store rows drag like Files rows; a + before back opens Load files (§5.5, §16.9, §24.2) by @js2264 in #117
• A 3D model leaves as a PDB for PyMOL, and a connected folder offers every file the app opens (§20.5, §25.2, §25.3, §25.7) by @js2264 in #119
• A 1D task is one Run, deck or not, and the star is nothing to it (§18.1, §18.4) by @js2264 in #118
• Record every number validation figures draw in validation.txt by @js2264 in #120
• Loop calling, a 2D task just before Pattern detection (§18.8, §18.9) by @js2264 in #121
• Switch to GPL-3.0-or-later and add licence attribution in About by @js2264 in #124
• Tutorial on K562 map with sequence copy and manual marks by @js2264 in #123

Full Changelog: v0.15.0...v0.16.0

v0.15.0

What's Changed

• Unify interface grammar across all reader-facing surfaces by @js2264 in #69
• pastis-NB, four analysis cards, and a deck cell per model (§18.8, §25.3, §25.5, §25.6) by @js2264 in #68
• Read a bed3d whose solver left bins unplaced as the structure it is (§25.2) by @js2264 in #70
• Metagenome sequences card and unified level control by @js2264 in #71
• The Map card follows the star, and no map or structure need be starred (§16.5, §25.3) by @js2264 in #73
• Add bacterial chromosome analysis: origins, arms, and group signal by @js2264 in #72
• Move synthetic tracks to Tracks card, add points style by @js2264 in #74
• Inter-arm alignment's table gives the enrichment, as a fold by @js2264 in #76
• Add peak calling task with yapc and IDR implementations by @js2264 in #75
• Open every map of a multi-file drop in its cell (§16.11) by @js2264 in #77
• Overlay map selection and validation notebook by @js2264 in #79
• Draw maps to a chosen number of contacts (§6.5) by @js2264 in #78
• Draw the inter-arm decay alone: inter-arm in the score picker on a circle (§7.5, §8.15) by @js2264 in #80
• P(s)'s four orientations: from the import, from a dropped .pairs, and unbroken (§18.8) by @js2264 in #81
• Reference editing: dev feature with stage, method, and exports by @js2264 in #82
• Chromosome ideograms and RNA-seq splice junctions as 1D tracks (§8.22, §8.23) by @js2264 in #83
• Open a large .hic without waiting on its contact count (§3.6, §6.5, §12) by @js2264 in #84
• Draw a chromosome clicked during the contact count in seconds (§6.5, §8.15, §9, §12) by @js2264 in #85
• Vector PDF export and 3D model support improvements by @js2264 in #86
• Inter-arm alignment: one row per sequence, reach to alignment edge by @js2264 in #87
• Reading frames, BAM base modifications, called sets as lanes, 3D by BED names, a live corner dot plot by @js2264 in #88
• Validation notebook: use public data with accessions by @js2264 in #89
• Cache reader answers to avoid re-reading visited maps by @js2264 in #90
• Decide a circle on two separations; a tab's note goes with its file (§8.15, §5.6) by @js2264 in #91
• Fold the columns from the digit row, step on the angle brackets, lock the map onto its diagonal, say how to zoom in, and scale the 1D browser's tracks together (§5.5, §5.8, §7.2, §8.9, §26.6) by @js2264 in #92
• Read a whole chromosome one bin to a pixel up to 16,384 bins a side (§7.2, §9, §16.7) by @js2264 in #93
• Add custom colour picker for all colour inputs by @js2264 in #95
• Light structures in PDF exports with shaded beads and banded tubes by @js2264 in #94
• Add pan and back/forward navigation controls by @js2264 in #96
• Hide and show the reader's marks, one or all, on every map, track and model (§8.1, §25.5) by @js2264 in #98
• Search a genome read by range for a motif, chromosome by chromosome, and open a --sequence by its index (§8.8, §8.21, §18.8, §23.1) by @js2264 in #99
• Draw a called set as one row, a 1D track or on the map as its display says; boundaries as points or short diagonal markers, domains as corners (§8.1, §18.5, §18.7, §18.8) by @js2264 in #100
• Track colouring: white-to-colour scale and editable key range by @js2264 in #101
• Rename the app chromosomix, rebuild the lab's data stores around the paper, bring workspaces back as saved, and add Figs. 1 and 2 by @js2264 in #103
• Fix figure window input and area fill behavior by @js2264 in #104
• Serve the site from chromosomix.app, and keep every archived build working there by @js2264 in #106
• Code review: CI oracles, security, CLI, capped readers, render cancellation, PDF paths, and the Session and MatrixPanel splits by @js2264 in #105
• APA as coolpuppy computes it, with O/E and a five-bin nearest loop by default; track correlation over exact windows, a missing one left out of every pair; chromosomix boost by @js2264 in #108
• Validation and timing notebooks, published at /validation/ and /timings/ with every release by @js2264 in #109
• Tab navigation, derived resolution tasks, and figure rendering by @js2264 in #110
• Faster DI, compartments, coverage and metaplot: Lanczos, rows from the index, held bigWig reads by @js2264 in #111
• Add name column toggle to map's Tracks card by @js2264 in #113
• Add guided tutorial for first-time users by @js2264 in #112
• The npm package, ready to publish; the README reworked; the site written for search engines and language models by @js2264 in #114

Full Changelog: v0.13.0...v0.15.0

v0.14.0

What's Changed

• Unify interface grammar across all reader-facing surfaces by @js2264 in #69
• pastis-NB, four analysis cards, and a deck cell per model (§18.8, §25.3, §25.5, §25.6) by @js2264 in #68
• Read a bed3d whose solver left bins unplaced as the structure it is (§25.2) by @js2264 in #70
• Metagenome sequences card and unified level control by @js2264 in #71
• The Map card follows the star, and no map or structure need be starred (§16.5, §25.3) by @js2264 in #73
• Add bacterial chromosome analysis: origins, arms, and group signal by @js2264 in #72
• Move synthetic tracks to Tracks card, add points style by @js2264 in #74
• Inter-arm alignment's table gives the enrichment, as a fold by @js2264 in #76
• Add peak calling task with yapc and IDR implementations by @js2264 in #75
• Open every map of a multi-file drop in its cell (§16.11) by @js2264 in #77
• Overlay map selection and validation notebook by @js2264 in #79
• Draw maps to a chosen number of contacts (§6.5) by @js2264 in #78
• Draw the inter-arm decay alone: inter-arm in the score picker on a circle (§7.5, §8.15) by @js2264 in #80
• P(s)'s four orientations: from the import, from a dropped .pairs, and unbroken (§18.8) by @js2264 in #81
• Reference editing: dev feature with stage, method, and exports by @js2264 in #82
• Chromosome ideograms and RNA-seq splice junctions as 1D tracks (§8.22, §8.23) by @js2264 in #83
• Open a large .hic without waiting on its contact count (§3.6, §6.5, §12) by @js2264 in #84
• Draw a chromosome clicked during the contact count in seconds (§6.5, §8.15, §9, §12) by @js2264 in #85
• Vector PDF export and 3D model support improvements by @js2264 in #86
• Inter-arm alignment: one row per sequence, reach to alignment edge by @js2264 in #87
• Reading frames, BAM base modifications, called sets as lanes, 3D by BED names, a live corner dot plot by @js2264 in #88
• Validation notebook: use public data with accessions by @js2264 in #89
• Cache reader answers to avoid re-reading visited maps by @js2264 in #90
• Decide a circle on two separations; a tab's note goes with its file (§8.15, §5.6) by @js2264 in #91
• Fold the columns from the digit row, step on the angle brackets, lock the map onto its diagonal, say how to zoom in, and scale the 1D browser's tracks together (§5.5, §5.8, §7.2, §8.9, §26.6) by @js2264 in #92
• Read a whole chromosome one bin to a pixel up to 16,384 bins a side (§7.2, §9, §16.7) by @js2264 in #93
• Add custom colour picker for all colour inputs by @js2264 in #95
• Light structures in PDF exports with shaded beads and banded tubes by @js2264 in #94
• Add pan and back/forward navigation controls by @js2264 in #96
• Hide and show the reader's marks, one or all, on every map, track and model (§8.1, §25.5) by @js2264 in #98
• Search a genome read by range for a motif, chromosome by chromosome, and open a --sequence by its index (§8.8, §8.21, §18.8, §23.1) by @js2264 in #99
• Draw a called set as one row, a 1D track or on the map as its display says; boundaries as points or short diagonal markers, domains as corners (§8.1, §18.5, §18.7, §18.8) by @js2264 in #100
• Track colouring: white-to-colour scale and editable key range by @js2264 in #101
• Rename the app chromosomix, rebuild the lab's data stores around the paper, bring workspaces back as saved, and add Figs. 1 and 2 by @js2264 in #103
• Fix figure window input and area fill behavior by @js2264 in #104
• Serve the site from chromosomix.app, and keep every archived build working there by @js2264 in #106
• Code review: CI oracles, security, CLI, capped readers, render cancellation, PDF paths, and the Session and MatrixPanel splits by @js2264 in #105
• APA as coolpuppy computes it, with O/E and a five-bin nearest loop by default; track correlation over exact windows, a missing one left out of every pair; chromosomix boost by @js2264 in #108
• Validation and timing notebooks, published at /validation/ and /timings/ with every release by @js2264 in #109
• Tab navigation, derived resolution tasks, and figure rendering by @js2264 in #110
• Faster DI, compartments, coverage and metaplot: Lanczos, rows from the index, held bigWig reads by @js2264 in #111
• Add name column toggle to map's Tracks card by @js2264 in #113
• Add guided tutorial for first-time users by @js2264 in #112
• The npm package, ready to publish; the README reworked; the site written for search engines and language models by @js2264 in #114

Full Changelog: v0.13.0...v0.14.0

v0.13.0

What's Changed

• Domain pileup APA and multi-scale insulation with heatmap rendering by @js2264 in #42
• Add CLI command export and card folding UI features by @js2264 in #43
• Publish a preview of every pull request on the Pages site by @js2264 in #45
• Remote sources beyond S3: hubs, portal search, share links, Google Drive and Dropbox by @js2264 in #44
• Publish the generated hubs through the site, because the repository is private by @js2264 in #48
• Five new analysis tasks, and two that could not answer a question they were for by @js2264 in #46
• Public stores: IGV's genomes, all of 4DN, all of ENCODE, and sessions with the tracks on by @js2264 in #50
• Three near-diagonal readings, a 4C coverage divisor, a ribbon lane — and circular sequences by @js2264 in #51
• Segments say which strand, which way and which column, on every interval lane by @js2264 in #52
• Divide a map of several ticked genomes by genome, not by contig by @js2264 in #49
• Rename hubs to stores and redesign store interface by @js2264 in #53
• Open files from one door: Drive and Dropbox sign-ins, index-free BAMs, Drive by name and by range, and stores that list only what draws by @js2264 in #54
• Enable all analysis tasks to run from CLI by supporting tracks and peer maps by @js2264 in #55
• Add legend toggle, deck export, and compartments resolution warnings by @js2264 in #56
• Give the four stores their marks, trim the picker and the Connect dialog, and stop a first visit eating a shared link by @js2264 in #57
• Add DNA Zoo front end and bucket folder naming support by @js2264 in #59
• Add barChart and bigBarChart support (§8.17) by @js2264 in #60
• Add folder mounting to landing page with new connect doors by @js2264 in #58
• Let a species with no README.json keep its files, as --readme optional says by @js2264 in #61
• Support bacterial GFF annotations with no hierarchy by @js2264 in #64
• Redefine HiC score as mean of bin's line across near-diagonal by @js2264 in #63
• Read five UCSC formats, and open a track hub as a store (§8.18–§8.21, §24.10) by @js2264 in #62
• Redesign landing page, unify button styles, and improve visual hierarchy by @js2264 in #65
• A 3D structure beside the map, and every figure restyles (§25, §18.13) by @js2264 in #66
• Resolutions the file does not store, zoom both ways from the bar, and an APA that pools its anchors by @js2264 in #67

Full Changelog: v0.12.0...v0.13.0

v0.12.0

Added

• Find a sequence — a new analysis task. Choose a loaded reference, type a
  motif, and every place it occurs comes back as two lanes. The pattern is
  IUPAC — GGTCANNNTGACC, GATC, TTAGGG — spaces are ignored, and both
  strands are searched unless you say otherwise; a palindrome is reported once
  rather than twice, because searching both strands of GAATTC would otherwise
  count every site again and a reader totting up a lane would get double the
  answer with nothing on screen to explain it.

  Two lanes, not one, and that is the point. A set of sites answers two
  questions and no single picture answers both: where exactly is it, which is
  an interval per site — clickable, strand-carrying, exportable as BED, and an
  eligible input to overlap, the metaplot and APA like any other interval set
  (§18.3) — and how dense is it here, which is sites per bin and is the only
  one of the two that means anything at chromosome scale. The first is a picket
  fence when you zoom out; the second is a bar chart of ones when you zoom in.

  Two decisions inside it are worth stating because they are the ones that
  would be wrong by default. An N in the reference does not satisfy a
  pattern that names a base: an assembly gap is a base nobody knows, not a base
  that is any of four, and matching it would turn every gap into a solid bar of
  fictional hits — most of what you would see on a draft genome. And an empty
  bin in the density lane is a zero, never a gap: NaN in a per-bin vector
  draws as a hole, and "there is no site here" is the answer, not missing data.

  It is a registered task rather than a card of its own, which is what earns it
  the parameter form, a recipe that travels in the session, provenance on both
  outputs, a place in the deck's all-maps overlay, and Recompute on a
  reload — none of which a bespoke card would have had, and all of which every
  other task already has. venue: 'annotations', because the residues are in
  that worker and nowhere else: a genome is parsed into it and deliberately
  never shipped out whole, so searching anywhere else would mean hauling
  megabytes across the boundary or stitching thirty windowed reads together at
  the seams. A run declines a pattern that is not IUPAC before it starts, with
  the character it could not read named.

  It works in a genome-browser session as well as over a map, which is the
  session a reader who came in through a FASTA is actually in. That took
  fixing something older: a session with no contact map reported its bin size
  as 0, a placeholder that was safe only while nothing producing a per-bin
  result could be run without a matrix. A task answering from the sequence
  broke that assumption, and a zero bin size gives every contig zero bins — a
  lane that is permanently empty rather than one that is visibly wrong,
  which is the failure nothing reports. A mapless session is now given a
  browsing grid chosen from the assembly's own length; it is a resolution to
  draw at and never a claim that anything was measured at it, so the tasks
  that genuinely need a matrix go on saying they are waiting for one.

• A fold button on every panel header. Each of the five columns now carries a
  chevron beside its shortcut chip, pointing the way that column travels — left
  for the three on the left, right for the two on the right. The affordance
  existed when a panel was folded (the rotated spine tab, which points the
  other way because it offers to open) and was missing when it was open, so the
  only way to close a column was a button in the header bar that does not look
  like it belongs to it. It goes through the same fold every other entry point
  does, so the remembered state, the relayout and the settle all happen once.

• Shift-click ticks a range in the Tracks card. Ticking the first ten of
  thirty tracks was ten clicks on an eleven-pixel box, which is the arithmetic
  that makes a batch action cost more than doing the ten by hand. Click one box,
  shift-click another, and every row between the two takes the state the clicked
  box is moving to — the gesture every file list has. The anchor is remembered as
  a row's id and resolved to a position at click time, because the rows are
  drag-reorderable and the card's list is not the store's: an index cached at the
  first click is a lie the moment anything moves.

• Z-score the tracks first, on the metaplot. A new option under Summary,
  off by default. Two tracks in different units — a CPM bigWig and a log2 ratio —
  plotted on one axis compare nothing; standardising each by its own mean and SD
  before the metric puts them on one scale. The statistics are taken per track
  and shared across that track's ranking groups, which is the part that is easy
  to get wrong: standardising each group separately would re-centre every one of
  them on zero and erase the ranking the reader split them by. A constant track
  is centred and not divided, so nothing comes back as ±∞, and gaps stay gaps.
  The heatmap shows the standardised values too, so the two halves of one figure
  cannot disagree, and the y axis is relabelled rather than left claiming a unit
  the numbers no longer have.

• The viewer is published to npm, as a built directory rather than as
  something to import — so a page can embed a copy that depends on nobody's
  hosting, including ours:

  <iframe src="https://cdn.jsdelivr.net/npm/metacooler-viewer@0.11.0/dist/index.html?embed=1&config=…"></iframe>

  npm pack metacooler-viewer && tar xf metacooler-viewer-*.tgz && cp -r package/dist /var/www/viewer/

  A sixth invocation of the same bundler (vite.package.config.ts), and the one
  built for a path it does not know. Everything else this repository emits is
  served from somewhere decided in advance — the site root, /v/<commit>/, an
  asar, a disk — and bakes absolute asset URLs accordingly. A tarball is
  unpacked wherever somebody puts it, so its base is ./ and one published
  version serves all of them. The rule that comes with that is the mounter's:
  the URL has to end in a slash, or name index.html.

  Two things follow from a copy not knowing where it is, and both are enforced
  rather than assumed (IS_PORTABLE): it registers no service worker, since
  a copy mounted under a path it does not own must not claim a scope there — on
  a registry CDN that scope covers other people's packages — and it asks for
  no version manifest, since versions.json lives at a site root a vendored
  copy has no way to find. Before those guards, every vendored copy would have
  made two doomed requests: a 404 for a sw.js this build does not emit, and a
  cross-origin fetch for a manifest belonging to somebody else's server.

  files is dist/ and dist-cli/, which is the whole of what stands between
  a publish and 250 MB of demo data, and which makes npx metacooler-run work
  against a published version with no clone. prepack builds and
  check-package-build.mjs then refuses the result if it is wrong — a tarball
  packed over a site build would carry absolute asset URLs that 404 on every
  mount but the site root, and unlike everything else here a published version
  cannot be corrected.

  private: true is gone with its comment. The argument it made — an
  application, not a library — is still true and is not what publishing changes:
  what a registry is wanted for here is hosting nobody has to trust, not
  dependency resolution. Specified at SPECS §22.

• A LICENSE file, with the MIT text the manifest has always declared. It
  was missing, which matters most at the moment a package is published: npm
  shows the licence of a package it can find one for, and a tarball that
  declares MIT without carrying it is asking to be taken on trust.

• .pairs files open, at a resolution you choose. A 4DN pairs file — plain,
  gzipped or bgzipped, with a .px2 beside it or without one — is now an
  accepted input, and it is the first one the app imports rather than opens.
  Everything else in §3 is a matrix in a container; a pairs file is a list of
  contacts, and there is no grid in it. So the first open is refused, a dialog
  asks for a base resolution and a number of ladder rungs, and the file is read
  once. After that it is a map like any other: the same views, the same deck,
  the same turn, the same fourteen analysis tasks, none of which learns the
  container exists.

  The grid could not be guessed, and that is why there is a dialog rather
  than a default. A bin table inferred from the largest coordinate observed
  would differ between two subsamples of the same library — the one way of being
  wrong that survives every check downstream and makes two files silently
  incomparable.

  The ladder is nearly free, so it is offered rather than rationed: the base
  rung costs a pass over the records, and every rung above it is derived from
  that table, which is smaller than the record stream by the ratio of records to
  stored pixels — thirteen to one on demo/yeast/. The rungs are spelled the
  way an .mcool's resolutions are, which wires them into the resolution
  picker, the refine ladder and a deck descending to its lead's rung with no
  code in any of them.

  The shape of the data is what makes this the right design. On this
  repository's own demo files, yeast Micro-C is 179 M records and 13.7 M stored
  pixels at 1 kb; the mock community is 10.9 M records and 7.1 M pixels. The
  input is gigabytes and the output is tens of megabytes — so the file is paid
  for once, at open, and every view afterwards costs no I/O at all.
  demo/ecoli/SRR19500734.pairs.gz — 238 MB, 17.7 M records — imports in about
  forty seconds.

  What decides that time is the file's BGZF framing rather than this code,
  and it is worth knowing because it can be changed. A deflate...

v0.10.0

Added

• Zooming sharpens the picture. A block larger than the screen has arrived
  coarsened since pooling landed — a whole yeast genome at 1 kb is drawn at
  3.0 kb cells, and the note under it said so honestly and told you the remedy
  was to open something smaller. That was true and it was not the interaction
  anybody has in their hands. A zoom that settles past what the block can
  show now reads that window again at the grid the picture could show: on the
  demo yeast cooler, 3.0 kb becomes 1.0 kb on one bounded read, and on a file
  that size the read comes out of the chunk cache without touching the network.

  It changes one clause of SPECS §2 and leaves three standing, which is the whole
  design. There is still no tile server, nothing is cut into tiles, and no
  picture is ever assembled out of parts: what is drawn is always exactly one
  bounded block. A gesture still costs nothing — the read goes out after the
  window stops moving, never during it, and neither the renderer nor the panel
  holds a reader to issue it with. It terminates, because there is no grid
  below the file's own bins: one step for a whole yeast genome, three for a human
  chromosome at 5 kb, and none at all for a MAG, whose block already is the
  finest data in the file — §2's own case is untouched. And it is bounded by
  the view: a zoom can never widen past the domain the view was entered on, so
  it cannot become the full pixel scan §7.3 gates.

  Zooming back out is served the same way and is usually free: two or three
  whole blocks are kept, so leaving what a fine one covers falls back to a coarse
  one still in hand. The colour range is measured from the widest of them and
  does not move while you zoom in — coarse cells are sums of bins, so a finer
  block holds smaller numbers, and re-measuring would re-brighten the map for
  somebody who changed nothing but the magnification.

  It refines under an O/E map, under two files blended on the diagonal, under a
  45° turn, and in every panel of a deck independently — the last of those
  because the navigation lock's currency was always base pairs, so five maps at
  five resolutions were already in step. The one picture that does not refine is
  the genome × genome overview, whose axes are sequences rather than positions:
  a cell there is a contig, and there is nothing finer to go to.

  The moment it happens is shown, not hidden. Crossing the edge of what the
  block can show freezes the map — no pan, no zoom — and puts a spinner in the
  corner of the plot until the new grid lands, so the picture is exactly where
  you left it when it sharpens and the change is one you can watch happen.
  Escape calls the read off and gives the map back, so no file can lock it.
  Panning to the edge of the block reads the next stretch at the same
  resolution: panning is a change of place, not of scale, and getting that
  wrong hands a reader back a four-times coarser map for dragging left.

  The key in the corner now names the cell size, on its own line, and in
  exported figures too. It is the one thing about a refining map that the pixels
  cannot tell you.

  Off by default, because a zoom that reads is a zoom that can wait and §2's
  promise has always been that it does not. The switch is the first of the three
  on the map's picture row — three bars, coarse at the top, fine at the bottom
  — beside the 45° turn and the O/E baseline, and Read finer data as you zoom
  in the command palette does the same thing. Off is exactly the old behaviour.
  The note under a pooled map now ends
  · zoom in to sharpen or · open a smaller block to sharpen depending on
  which. MULTIRES-ZOOM.md is the study this came out of, with a closing section
  on where the built thing differs from the plan.

• The resolution ladder drives the zoom (§3.4, §9). "Wire the entries to the
  zoom control" has been in the spec since the first draft and in README's own
  list of gaps as inferred but not driven. A zoom now reads from the
  coarsest rung of an .mcool or .mmetacool whose bins still fill a cell — and
  never one finer than the level you opened, which is a choice the zoom does not
  get to overrule:
  fewer stored pixels for the same picture, and — the reason that matters — a
  balanced map that was balanced at that resolution rather than summed, which
  is what zoomify --balance produces and what the reader has been calling "the
  real answer" in a comment since pooling landed.

  The rungs a zoom touches are opened beside the one that is open, over the same
  mounted bytes, bounded at three and released with the session; a navigation
  still closes the map, because a navigation means the last place is finished
  with. Bin indices are not comparable between levels — five chromosomes of the
  demo .mcool have one fewer 2 kb bin than the division says — so windows cross
  through base pairs, per contig, with a whole sequence converting to its whole
  self at either end. None of it is required: a plain .metacool has no ladder
  and the zoom reads the open map, which is §3.4's own rule for what a ladder is
  allowed to be.

• A 4C profile can be divided by P(s). A slice of a Hi-C map is mostly P(s):
  contact falls by orders of magnitude with distance, so a raw 4C profile's shape
  is dominated by how far away each bin is rather than by whether anything is
  happening there — a clean triangle with the anchor at its apex, on which the
  loops somebody ran the task to find are bumps visible near the anchor and
  invisible a megabase out. The task now offers a Normalisation choice: none,
  which stays the default because the raw profile is what a bigWig of a 4C
  experiment holds, or by P(s), which reports observed over expected at each
  separation.

  The decay is taken from the anchor's own sequence, accumulated from the
  square the task is already reading, rather than from the P(s) task's
  genome-wide curve: a small chromosome divided by the average behaviour of the
  large ones comes out with a slope that is a property of the set rather than of
  the locus. Bins in trans are divided by the mean of what the anchor reaches off
  its own sequence, since "separation" means nothing between chromosomes.

• Synthetic tracks survive a change of resolution. Switching an .mcool from
  1 kb to 5 kb is not opening a different file — it is the same data at a
  different bin size — and everything a reader can see already treated it that
  way: the view carries across, and so does every dropped track. The one thing
  that did not was the output of an analysis. Run compartments genome-wide, wait
  the four minutes, change level to look at the same region more closely, and the
  Synthetic tracks card was empty: numbers the tab was still holding, dropped for
  no reason other than which object held them.

  They now come across live, as the rows the reader left — the colour, the name,
  the edge, the autoscale group, whether it was hidden — with the values still
  behind them and the exports still on them. Unrescaled, which is the honest
  thing and not a shortcut: a profile is one number per bin, its bins were 1 kb,
  and the row goes on saying so in its provenance line. Re-binning it to 5 kb
  would be inventing an insulation score no window ever produced. What makes that
  work is that a computed vector has always carried its own grid — the same
  reason a bigWig at one resolution draws correctly over a map at another.

  Called interval sets — insulation boundaries, CID domains, A/B compartments —
  come across the same way, with their features and their Save as BED. A row
  that was already waiting for a Recompute stays waiting for one rather than
  being promoted to a lane with nothing in it. And this is for a change of
  resolution only: opening a different file still leaves the analysis behind,
  because a computed row is an answer about the file being closed.

• The Chromosomes table gets the browser's bar, and you can drag out a
  window. The table is where a reader of a cooler lands, and the only way out
  of it into a window was to type one — a row click opens a whole chromosome,
  and a quarter of a gigabase is a large read taken to reach a small one. The box
  that narrowed it asked for chrIV:1200000-1210000, which is a coordinate
  somebody is usually looking for rather than one they already have.

  So the header is now the 1D browser's own: the same locus box, with the same
  gene search behind it — by name or by accession, from whichever annotation the
  star picks — the same go, the same switch through to the tracks, and the
  same ruler. Dragging across a chromosome's band opens that window, which is
  the gesture the picture was missing; a press that does not travel opens the
  whole sequence under it, and * opens the whole genome as it does in the
  browser.

  The strip answers a pointer the way the browser's own does: a hairline
  follows it and the cursor is a caret. A band is fifty pixels of shading
  with a name in the middle, so without a line there is no way to see where in it
  a drag would start — on a chromosome an inch wide, a megabase of ambiguity —
  and the caret says the gesture names a stretch rather than moving an edge. The
  head above it is the bar and nothing else: the title and its sentence of prose
  are what a view needs when the reader has to be told where they are, and the
  breadcrumb, the ruler and the summary line all say it better.

  A band being dragged out looks exactly like one in the browser, from the
  same implementation: the wash, both edges as hairlines, and three chips — where
  the drag started, where the pointer is, and how much lies between. Those
  numbers are ...