@gmod/bam 7.1.18 → 7.1.20

package/CHANGELOG.md

@@ -1,532 +0,0 @@
-## [7.1.18](https://github.com/GMOD/bam-js/compare/v7.1.17...v7.1.18) (2026-03-04)
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-
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-## [7.1.17](https://github.com/GMOD/bam-js/compare/v7.1.16...v7.1.17) (2026-02-14)
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-
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-## [7.1.16](https://github.com/GMOD/bam-js/compare/v7.1.15...v7.1.16) (2026-02-14)
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-
-## [7.1.15](https://github.com/GMOD/bam-js/compare/v7.1.14...v7.1.15) (2025-12-17)
-
-## [7.1.14](https://github.com/GMOD/bam-js/compare/v7.1.13...v7.1.14) (2025-12-17)
-
-## [7.1.13](https://github.com/GMOD/bam-js/compare/v7.1.12...v7.1.13) (2025-12-17)
-
-## [7.1.12](https://github.com/GMOD/bam-js/compare/v7.1.11...v7.1.12) (2025-12-17)
-
-## [7.1.11](https://github.com/GMOD/bam-js/compare/v7.1.10...v7.1.11) (2025-12-16)
-
-## [7.1.10](https://github.com/GMOD/bam-js/compare/v7.1.9...v7.1.10) (2025-12-15)
-
-## [7.1.9](https://github.com/GMOD/bam-js/compare/v7.1.8...v7.1.9) (2025-12-13)
-
-## [7.1.8](https://github.com/GMOD/bam-js/compare/v7.1.7...v7.1.8) (2025-12-13)
-
-## [7.1.7](https://github.com/GMOD/bam-js/compare/v7.1.6...v7.1.7) (2025-12-13)
-
-## [7.1.6](https://github.com/GMOD/bam-js/compare/v7.1.5...v7.1.6) (2025-12-13)
-
-## [7.1.5](https://github.com/GMOD/bam-js/compare/v7.1.4...v7.1.5) (2025-12-13)
-
-## [7.1.4](https://github.com/GMOD/bam-js/compare/v7.1.3...v7.1.4) (2025-12-13)
-
-## [7.1.3](https://github.com/GMOD/bam-js/compare/v7.1.2...v7.1.3) (2025-12-12)
-
-## [7.1.2](https://github.com/GMOD/bam-js/compare/v7.1.1...v7.1.2) (2025-12-12)
-
-## [7.1.1](https://github.com/GMOD/bam-js/compare/v7.1.0...v7.1.1) (2025-12-12)
-
-# [7.1.0](https://github.com/GMOD/bam-js/compare/v7.0.6...v7.1.0) (2025-12-11)
-
-## [7.0.6](https://github.com/GMOD/bam-js/compare/v7.0.5...v7.0.6) (2025-11-28)
-
-## [7.0.5](https://github.com/GMOD/bam-js/compare/v7.0.4...v7.0.5) (2025-11-27)
-
-## [7.0.4](https://github.com/GMOD/bam-js/compare/v7.0.3...v7.0.4) (2025-11-24)
-
-## [7.0.3](https://github.com/GMOD/bam-js/compare/v7.0.2...v7.0.3) (2025-11-24)
-
-## [7.0.2](https://github.com/GMOD/bam-js/compare/v7.0.1...v7.0.2) (2025-11-24)
-
-## [7.0.1](https://github.com/GMOD/bam-js/compare/v7.0.0...v7.0.1) (2025-11-24)
-
-- Added NUMERIC_SEQ to get the raw encoded seq array
-
-# [7.0.0](https://github.com/GMOD/bam-js/compare/v6.1.1...v7.0.0) (2025-11-24)
-
-- Introduced the idea of returning TypedArrays for different tag types
-
-## [6.1.1](https://github.com/GMOD/bam-js/compare/v6.1.0...v6.1.1) (2025-10-02)
-
-# [6.1.0](https://github.com/GMOD/bam-js/compare/v6.0.4...v6.1.0) (2025-10-01)
-
-## [6.0.4](https://github.com/GMOD/bam-js/compare/v6.0.3...v6.0.4) (2025-05-26)
-
-## [6.0.3](https://github.com/GMOD/bam-js/compare/v6.0.2...v6.0.3) (2025-05-13)
-
-## [6.0.2](https://github.com/GMOD/bam-js/compare/v6.0.1...v6.0.2) (2025-04-30)
-
-## [6.0.1](https://github.com/GMOD/bam-js/compare/v6.0.0...v6.0.1) (2025-04-30)
-
-# [6.0.0](https://github.com/GMOD/bam-js/compare/v5.0.7...v6.0.0) (2025-04-30)
-
-## [5.0.7](https://github.com/GMOD/bam-js/compare/v5.0.6...v5.0.7) (2025-03-11)
-
-## [5.0.6](https://github.com/GMOD/bam-js/compare/v5.0.5...v5.0.6) (2025-02-28)
-
-## [5.0.5](https://github.com/GMOD/bam-js/compare/v5.0.4...v5.0.5) (2024-12-18)
-
-## [5.0.4](https://github.com/GMOD/bam-js/compare/v5.0.2...v5.0.4) (2024-12-18)
-
-## [5.0.3](https://github.com/GMOD/bam-js/compare/v5.0.2...v5.0.3) (2024-12-18)
-
-## [5.0.2](https://github.com/GMOD/bam-js/compare/v5.0.1...v5.0.2) (2024-12-17)
-
-## [5.0.1](https://github.com/GMOD/bam-js/compare/v5.0.0...v5.0.1) (2024-12-12)
-
-# [5.0.0](https://github.com/GMOD/bam-js/compare/v4.0.1...v5.0.0) (2024-12-12)
-
-## [4.0.1](https://github.com/GMOD/bam-js/compare/v4.0.0...v4.0.1) (2024-11-12)
-
-# [4.0.0](https://github.com/GMOD/bam-js/compare/v3.0.3...v4.0.0) (2024-11-12)
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-## [3.0.3](https://github.com/GMOD/bam-js/compare/v3.0.0...v3.0.3) (2024-11-11)
-
-## [3.0.2](https://github.com/GMOD/bam-js/compare/v3.0.0...v3.0.2) (2024-11-11)
-
-- republish v3.0.1 since it got tagged on a deleted branch
-
-## [3.0.1](https://github.com/GMOD/bam-js/compare/v3.0.0...v3.0.1) (2024-11-11)
-
-# [3.0.0](https://github.com/GMOD/bam-js/compare/v2.0.4...v3.0.0) (2024-11-07)
-
-## [2.0.4](https://github.com/GMOD/bam-js/compare/v2.0.3...v2.0.4) (2024-08-09)
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-## [2.0.3](https://github.com/GMOD/bam-js/compare/v2.0.2...v2.0.3) (2024-07-23)
-
-### Reverts
-
-- Revert "Migrate to eslint9"
-  ([65adcbb](https://github.com/GMOD/bam-js/commit/65adcbb2793243659682d30694f8604d241a5337))
-- Revert "Run format"
-  ([2a02535](https://github.com/GMOD/bam-js/commit/2a02535db4df80f245232522cdba771cbf5ea214))
-
-## [2.0.2](https://github.com/GMOD/bam-js/compare/v2.0.1...v2.0.2) (2024-02-21)
-
-- Update typescript-eslint config and related fixes
-
-## [2.0.1](https://github.com/GMOD/bam-js/compare/v2.0.0...v2.0.1) (2024-2-20)
-
-- Update to buffer-crc32 1.0.0
-- Fix BAM header parsing of refNames containing a :
-
-# [2.0.0](https://github.com/GMOD/bam-js/compare/v1.1.18...v2.0.0) (2023-06-08)
-
-### Features
-
-- explicit buffer import ([#98](https://github.com/GMOD/bam-js/issues/98))
-  ([66de9f4](https://github.com/GMOD/bam-js/commit/66de9f4ce30e3ff647d5297f093695e92ec9227c))
-
-* Add explicit buffer import
-* Remove cross-fetch and object.entries polyfills
-* Improve typescripting
-* Remove chunkSizeLimit and fetchSizeLimit
-
-## [1.1.18](https://github.com/GMOD/bam-js/compare/v1.1.17...v1.1.18) (2022-12-17)
-
-- Use es2015 for nodejs build
-
-## [1.1.17](https://github.com/GMOD/bam-js/compare/v1.1.16...v1.1.17) (2022-07-18)
-
-- Bump devDeps and generic-filehandle to 3.0.0
-
-## [1.1.16](https://github.com/GMOD/bam-js/compare/v1.1.15...v1.1.16) (2022-03-30)
-
-- Add src directory for better source maps
-
-## [1.1.15](https://github.com/GMOD/bam-js/compare/v1.1.14...v1.1.15) (2022-03-18)
-
-- Fix for htsget failing with message 'input must be buffer, number, or string,
-  received object'
-- Speed improvement by caching chunks of features
-
-## [1.1.14](https://github.com/GMOD/bam-js/compare/v1.1.13...v1.1.14) (2022-03-14)
-
-- Fix seq function for corner case
-
-## [1.1.13](https://github.com/GMOD/bam-js/compare/v1.1.12...v1.1.13) (2022-02-25)
-
-- Optimize qual and sequence string record functions for less GC pressure
-
-<a name="1.1.12"></a>
-
-## [1.1.12](https://github.com/GMOD/bam-js/compare/v1.1.11...v1.1.12) (2022-02-17)
-
-- Add blocksForRange method to BamFile class to help stats estimation in JBrowse
-  2
-
-<a name="1.1.11"></a>
-
-## [1.1.11](https://github.com/GMOD/bam-js/compare/v1.1.10...v1.1.11) (2022-01-26)
-
-- Cache setup of index file parsing
-
-<a name="1.1.10"></a>
-
-## [1.1.10](https://github.com/GMOD/bam-js/compare/v1.1.9...v1.1.10) (2022-01-18)
-
-- Make \_refID and flags public fields
-- Small internal changes to the handling of opts
-
-<a name="1.1.9"></a>
-
-## [1.1.9](https://github.com/GMOD/bam-js/compare/v1.1.8...v1.1.9) (2021-12-14)
-
-- Add ESM module export in package.json (smaller bundle size for consumers)
-- Cache BAI readFile result for compatibility with node.js native filehandles
-  (which otherwise fail if re-reading the filehandle twice)
-
-<a name="1.1.8"></a>
-
-## [1.1.8](https://github.com/GMOD/bam-js/compare/v1.1.7...v1.1.8) (2021-05-21)
-
-- Fix types for yieldThreadTime
-
-<a name="1.1.7"></a>
-
-## [1.1.7](https://github.com/GMOD/bam-js/compare/v1.1.6...v1.1.7) (2021-05-21)
-
-- New param yieldThreadTime to constructor to yield while processing
-
-<a name="1.1.6"></a>
-
-## [1.1.6](https://github.com/GMOD/bam-js/compare/v1.1.5...v1.1.6) (2021-02-20)
-
-- Add qualRaw function on records for getting raw qual score array instead of
-  string
-
-<a name="1.1.5"></a>
-
-## [1.1.5](https://github.com/GMOD/bam-js/compare/v1.1.4...v1.1.5) (2020-12-11)
-
-- Allow getHeaderText to accept cancellation options
-
-<a name="1.1.4"></a>
-
-## [1.1.4](https://github.com/GMOD/bam-js/compare/v1.1.3...v1.1.4) (2020-12-11)
-
-- Add canMergeBlocks to CSI code (already existed in BAI)
-- Add suggestion from @jrobinso about reg2bins modification for memory saving
-  (Thanks!)
-- Add getHeaderText() method for getting a text string of the header data
-
-<a name="1.1.3"></a>
-
-## [1.1.3](https://github.com/GMOD/bam-js/compare/v1.1.2...v1.1.3) (2020-10-29)
-
-- Fix usage of feature.get('seq'), was using feature.getReadBases before this
-
-<a name="1.1.2"></a>
-
-## [1.1.2](https://github.com/GMOD/bam-js/compare/v1.1.1...v1.1.2) (2020-10-02)
-
-- Fix signedness in BAM tags (#65)
-- Remove unused seq_reverse_complemented tag from \_tags()
-
-<a name="1.1.1"></a>
-
-## [1.1.1](https://github.com/GMOD/bam-js/compare/v1.1.0...v1.1.1) (2020-09-20)
-
-- Remove JBrowse specific results from tags
-
-<a name="1.1.0"></a>
-
-# [1.1.0](https://github.com/GMOD/bam-js/compare/v1.0.42...v1.1.0) (2020-08-28)
-
-- Add support for the CG tag for long CIGAR strings
-
-<a name="1.0.42"></a>
-
-## [1.0.42](https://github.com/GMOD/bam-js/compare/v1.0.41...v1.0.42) (2020-08-19)
-
-- Small bugfix for Htsget specifically
-
-<a name="1.0.41"></a>
-
-## [1.0.41](https://github.com/GMOD/bam-js/compare/v1.0.40...v1.0.41) (2020-08-19)
-
-- Add htsget example
-- Support opts object to getHeader allowing things like auth headers to be
-  passed right off the bat
-
-<a name="1.0.40"></a>
-
-## [1.0.40](https://github.com/GMOD/bam-js/compare/v1.0.39...v1.0.40) (2020-07-30)
-
-<a name="1.0.39"></a>
-
-## [1.0.39](https://github.com/GMOD/bam-js/compare/v1.0.38...v1.0.39) (2020-07-30)
-
-- Don't use origin master in the follow-tags postpublish command for cleaner
-  version publishing
-
-<a name="1.0.38"></a>
-
-## [1.0.38](https://github.com/GMOD/bam-js/compare/v1.0.37...v1.0.38) (2020-07-30)
-
-- Direct construction of qual/seq toString
-- Improve performance of the uniqueID calculation for pathological cases where
-  there are tons of bins
-
-<a name="1.0.37"></a>
-
-## [1.0.37](https://github.com/GMOD/bam-js/compare/v1.0.36...v1.0.37) (2020-06-06)
-
-- Typescript only release: export BamRecord types
-
-<a name="1.0.36"></a>
-
-## [1.0.36](https://github.com/GMOD/bam-js/compare/v1.0.35...v1.0.36) (2020-03-05)
-
-- Adds a shortcut to stop parsing chunks after a record is detected to be
-  outside the requested range while decoding
-
-<a name="1.0.35"></a>
-
-## [1.0.35](https://github.com/GMOD/bam-js/compare/v1.0.34...v1.0.35) (2020-02-04)
-
-- Update scheme used to calculate unique fileOffset based IDs using
-  @gmod/bgzf-filehandle updates
-
-<a name="1.0.34"></a>
-
-## [1.0.34](https://github.com/GMOD/bam-js/compare/v1.0.33...v1.0.34) (2020-01-24)
-
-- Small fix for using id() instead of .get('id') for weird SAM records
-  containing ID field
-
-<a name="1.0.33"></a>
-
-## [1.0.33](https://github.com/GMOD/bam-js/compare/v1.0.32...v1.0.33) (2020-01-24)
-
-- Perform decoding of entire chunk up front to aid caching, reverts change in
-  1.0.29
-
-<a name="1.0.32"></a>
-
-## [1.0.32](https://github.com/GMOD/bam-js/compare/v1.0.31...v1.0.32) (2019-11-16)
-
-- Add a speed improvement for long reads by pre-allocating sequence/quality
-  scores array
-
-<a name="1.0.31"></a>
-
-## [1.0.31](https://github.com/GMOD/bam-js/compare/v1.0.30...v1.0.31) (2019-11-07)
-
-- Fix example of the "ID" field failing to return the right data
-
-<a name="1.0.30"></a>
-
-## [1.0.30](https://github.com/GMOD/bam-js/compare/v1.0.29...v1.0.30) (2019-11-07)
-
-- Add fix that was causing the parser to not return all tags from the \_tags API
-
-<a name="1.0.29"></a>
-
-## [1.0.29](https://github.com/GMOD/bam-js/compare/v1.0.28...v1.0.29) (2019-10-31)
-
-- Decoding of the BAM records at time of use instead of entire chunk decoded up
-  front
-- Alternate chunk merging strategy inspired by igv.js code
-
-<a name="1.0.28"></a>
-
-## [1.0.28](https://github.com/GMOD/bam-js/compare/v1.0.27...v1.0.28) (2019-10-29)
-
-- Add CSI index block merging
-- Change unique ID generator to be smaller numeric IDs
-
-<a name="1.0.27"></a>
-
-## [1.0.27](https://github.com/GMOD/bam-js/compare/v1.0.26...v1.0.27) (2019-10-10)
-
-- Make feature IDs become generated based relative to the exact bgzip block
-
-<a name="1.0.26"></a>
-
-## [1.0.26](https://github.com/GMOD/bam-js/compare/v1.0.25...v1.0.26) (2019-10-01)
-
-- Restore issue with getRecordsForRange not returning all features (#44)
-- Fix compatibility with electron (#43)
-- Fix usage of feature.get('seq')
-
-<a name="1.0.25"></a>
-
-## [1.0.25](https://github.com/GMOD/bam-js/compare/v1.0.24...v1.0.25) (2019-09-29)
-
-- Fixed some typescript typings
-
-<a name="1.0.24"></a>
-
-## [1.0.24](https://github.com/GMOD/bam-js/compare/v1.0.22...v1.0.24) (2019-09-27)
-
-- Added typescript typings
-
-<a name="1.0.23"></a>
-
-## [1.0.22](https://github.com/GMOD/bam-js/compare/v1.0.20...v1.0.22) (2019-09-27)
-
-- Added typescript typings
-- Botched release, was removed from npm
-
-<a name="1.0.22"></a>
-
-## [1.0.22](https://github.com/GMOD/bam-js/compare/v1.0.20...v1.0.22) (2019-09-03)
-
-- Fixed issue with features having different IDs across different chunks (#36)
-
-<a name="1.0.21"></a>
-
-## [1.0.21](https://github.com/GMOD/bam-js/compare/v1.0.20...v1.0.21) (2019-08-06)
-
-- Add a fix for the small chunk unpacking re-seeking in the same bgzf block
-  repeatedly (#35)
-
-<a name="1.0.20"></a>
-
-## [1.0.20](https://github.com/GMOD/bam-js/compare/v1.0.19...v1.0.20) (2019-06-06)
-
-- Added a method for smaller chunk unpacking, by modifying the header parsing to
-  return smaller chunks and the bgzf unzipping to respect chunk boundaries (#30)
-- Use fileOffset as bam feature ID which previously was crc32 of the BAM buffer
-  which consequently speeds up processing and allows exact duplicate features
-
-## [1.0.19](https://github.com/GMOD/bam-js/compare/v1.0.18...v1.0.19) (2019-05-30)
-
-- Added lineCount and hasRefSeq functions to BamFile, each accepting a string
-  seqName
-- Fixed aborting on index retrieval code
-
-## [1.0.18](https://github.com/GMOD/bam-js/compare/v1.0.17...v1.0.18) (2019-05-01)
-
-- Bump generic-filehandle to 1.0.9 to fix error with using native fetch (global
-  fetch needed to be bound)
-- Bump abortable-promise-cache to 1.0.1 version to fix error with using native
-  fetch and abort signals
-
-## [1.0.17](https://github.com/GMOD/bam-js/compare/v1.0.16...v1.0.17) (2019-04-28)
-
-- Fix wrong number of arguments being passed to the readRefSeqs file read()
-  invocation resulting in bad range requests
-
-## [1.0.16](https://github.com/GMOD/bam-js/compare/v1.0.15...v1.0.16) (2019-04-28)
-
-- Added indexCov algorithm to retrieve approximate coverage of the BAM inferred
-  from the size of the BAI linear index bins
-- Fixed abortSignal on read() calls
-- Updated API to allow bamUrl/baiUrl/csiUrl
-
-## [1.0.15](https://github.com/GMOD/bam-js/compare/v1.0.14...v1.0.15) (2019-04-04)
-
-- Added check for too large of chromosomes in the bai bins
-- Added aborting support (thanks @rbuels)
-- Refactored index file class
-
-<a name="1.0.14"></a>
-
-## [1.0.14](https://github.com/GMOD/bam-js/compare/v1.0.13...v1.0.14) (2019-01-04)
-
-- Add hasRefSeq for CSI indexes
-
-<a name="1.0.13"></a>
-
-## [1.0.13](https://github.com/GMOD/bam-js/compare/v1.0.12...v1.0.13) (2018-12-25)
-
-- Use ascii decoding for read names
-- Fix error with large BAM headers with many refseqs
-
-<a name="1.0.12"></a>
-
-## [1.0.12](https://github.com/GMOD/bam-js/compare/v1.0.11...v1.0.12) (2018-11-25)
-
-- Faster viewAsPairs operation
-
-<a name="1.0.11"></a>
-
-## [1.0.11](https://github.com/GMOD/bam-js/compare/v1.0.10...v1.0.11) (2018-11-23)
-
-- Fix for ie11
-
-<a name="1.0.10"></a>
-
-## [1.0.10](https://github.com/GMOD/bam-js/compare/v1.0.9...v1.0.10) (2018-11-18)
-
-- Add a maxInsertSize parameter to getRecordsForRange
-
-<a name="1.0.9"></a>
-
-## [1.0.9](https://github.com/GMOD/bam-js/compare/v1.0.8...v1.0.9) (2018-11-16)
-
-- Allow bases other than ACGT to be decoded
-- Make viewAsPairs only resolve pairs on given refSeq unless pairAcrossChr is
-  enabled for query
-
-<a name="1.0.8"></a>
-
-## [1.0.8](https://github.com/GMOD/bam-js/compare/v1.0.7...v1.0.8) (2018-10-31)
-
-- Add getPairOrientation for reads
-
-<a name="1.0.7"></a>
-
-## [1.0.7](https://github.com/GMOD/bam-js/compare/v1.0.6...v1.0.7) (2018-10-19)
-
-- Re-release of 1.0.6 due to build machinery error
-
-<a name="1.0.6"></a>
-
-## [1.0.6](https://github.com/GMOD/bam-js/compare/v1.0.5...v1.0.6) (2018-10-19)
-
-- Add bugfix for where bytes for an invalid request returns 0 resulting in pako
-  unzip errors
-
-<a name="1.0.5"></a>
-
-## [1.0.5](https://github.com/GMOD/bam-js/compare/v1.0.4...v1.0.5) (2018-10-16)
-
-- Add a bugfix for pairing reads related to adding duplicate records to results
-
-<a name="1.0.4"></a>
-
-## [1.0.4](https://github.com/GMOD/bam-js/compare/v1.0.3...v1.0.4) (2018-10-13)
-
-- Support pairing reads
-- Fix pseudobin parsing containing feature count on certain BAM files
-
-<a name="1.0.3"></a>
-
-## [1.0.3](https://github.com/GMOD/bam-js/compare/v1.0.2...v1.0.3) (2018-09-25)
-
-- Remove @gmod/tabix dependency
-
-<a name="1.0.2"></a>
-
-## [1.0.2](https://github.com/GMOD/bam-js/compare/v1.0.1...v1.0.2) (2018-09-25)
-
-- Fix CSI indexing code
-
-<a name="1.0.1"></a>
-
-## [1.0.1](https://github.com/GMOD/bam-js/compare/v1.0.0...v1.0.1) (2018-09-24)
-
-- Rename hasDataForReferenceSequence to hasRefSeq
-
-<a name="1.0.0"></a>
-
-# 1.0.0 (2018-09-24)
-
-- Initial implementation of BAM parsing code