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v1.5.0 Prep (#721)
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* Update schema changelog.
* Updated changelog for R and python packages
* R package version bump
* Update germline example in R package.
* Rebuild R docs

---------

Co-authored-by: Christian Busse <[email protected]>
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javh and bussec authored Aug 28, 2023
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5 changes: 5 additions & 0 deletions docs/packages/airr-R/news.rst
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Release Notes
=============

Version 1.5.0: August 28, 2023
------------------------------

- Updated schema set and examples to v1.5.

Version 1.4.1: August 27, 2022
------------------------------

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2 changes: 1 addition & 1 deletion docs/packages/airr-R/overview.rst
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.. _ROverview:

R Library
AIRR R Reference Library
=================================================================================

``airr`` is an R package for working with data formatted according to
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1 change: 1 addition & 0 deletions docs/packages/airr-R/topics/read_tabular.rst
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Expand Up @@ -69,6 +69,7 @@ Examples
# Load data file
df <- read_rearrangement(file)
See also
~~~~~~~~
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1 change: 0 additions & 1 deletion docs/packages/airr-R/topics/validate_tabular.rst
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Expand Up @@ -51,7 +51,6 @@ Examples
# Load data file
df <- read_rearrangement(file)
.. code:: r
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4 changes: 2 additions & 2 deletions docs/packages/airr-R/topics/write_tabular.rst
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Expand Up @@ -62,15 +62,15 @@ Examples
# Load data file
df <- read_rearrangement(file)
.. code:: r
# Write a Rearrangement data file
outfile <- file.path(tempdir(), "output.tsv")
write_tabular(df, outfile, schema=RearrangementSchema)
See also
~~~~~~~~
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68 changes: 34 additions & 34 deletions docs/packages/airr-R/vignettes/Usage-Vignette.rst
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Expand Up @@ -50,7 +50,7 @@ usage is straightforward, as the file format is a typical tabulated
file. The argument that needs attention is ``base``, with possible
values ``"0"`` and ``"1"``. ``base`` denotes the starting index for
positional fields in the input file. Positional fields are those that
contain alignment coordinates and names ending in "_start" and "_end".
contain alignment coordinates and names ending in “\_start” and “\_end”.
If the input file is using 1-based closed intervals (R style), as
defined by the standard, then positional fields will not be modified
under the default setting of ``base="1"``. If the input file is using
Expand All @@ -76,39 +76,39 @@ Reading Rearrangements

## Rows: 101
## Columns: 33
## $ sequence_id <chr> "SRR765688.7787", "SRR765688.35420", "SRR765688.36681", "SRR765688.33811", "SRR765688.44149", "SRR765688.15636", "SRR765688.20304", "SRR765688.13860", "SRR7656…
## $ sequence <chr> "NNNNNNNNNNNNNNNNNNNNGCTGACCTGCACCTTCTCTGGATTCTCACTCAGTACTAGTGCAGTGGGTGTACACTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGCCAAATATTACAGCACCAGCCC…
## $ rev_comp <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE…
## $ productive <lgl> TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, FALSE, TRUE, FALSE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE…
## $ vj_in_frame <lgl> TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, T…
## $ stop_codon <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FAL…
## $ v_call <chr> "IGHV2-5*02", "IGHV5-51*01", "IGHV7-4-1*02", "IGHV7-4-1*02", "IGHV7-4-1*02", "IGHV2-5*02", "IGHV7-4-1*02", "IGHV6-1*01,IGHV6-1*02", "IGHV7-4-1*02", "IGHV4-39*0…
## $ d_call <chr> "IGHD5-24*01", "IGHD3-16*02,IGHD3-3*01,IGHD3-3*02", "IGHD3-22*01", "IGHD3-9*01", "IGHD1-26*01", "IGHD2-21*02", "IGHD1-26*01,IGHD2-21*02,IGHD3/OR15-3a*01", "IGH…
## $ j_call <chr> "IGHJ4*02", "IGHJ6*02,IGHJ6*04", "IGHJ4*02", "IGHJ6*02", "IGHJ6*01", "IGHJ4*02", "IGHJ5*02", "IGHJ4*02", "IGHJ4*02", "IGHJ4*02", "IGHJ5*02", "IGHJ6*02", "IGHJ6…
## $ c_call <chr> "IGHG", "IGHG", "IGHG", "IGHG", "IGHG", "IGHA", "IGHA", "IGHG", "IGHG", "IGHA", "IGHA", "IGHG", "IGHA", "IGHA", "IGHG", "IGHA", "IGHG", "IGHA", "IGHG", "IGHG",…
## $ sequence_alignment <chr> "...........................................................GCTGACCTGCACCTTCTCTGGATTCTCACTCAGT......ACTAGTGCAGTGGGTGTACACTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCT…
## $ germline_alignment <chr> "CAGATCACCTTGAAGGAGTCTGGTCCT...ACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGC......ACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCT…
## $ junction <chr> "TGTGCACACAGTGCGGGATGGCTGCCTGATTACTGG", "TGTGCGAGGCATGGATTATACGGTTGTGATCATACCGGCTGTTATACAAGCTTCTACTACTACGGGATGGACGTCTGG", "TGTGCGAGAGAAGAACGTCGAAGTAGTGGTTATTTT…
## $ junction_aa <chr> "CAHSAGWLPDYW", "CARHGLYGCDHTGCYTSFYYYGMDVW", "CAREERRSSGYFDHW", "CAREGYYFDTTGSPRSHGLDVW", "CARDSGGMDVW", "CVLSRRLGDSGVQKYYFDYW", "CAREGLWDGRVVTDLW", "CARTRYSS…
## $ v_cigar <chr> "20S56N21=1X11=1X7=1X9=3X62=6D2=1X1=2X2=2X50=1X7=1X4=1X22=1X30=", "20S40N15=1X15=1X11=1X2=1X1=1X1=2X3=1X7=1X41=2X2=1X10=1X3=1X1=1X5=2X5=1X4=1X9=1X19=1X24=2X9=1…
## $ d_cigar <chr> "274S5N7=", "305S29N7=", "293S13N12=", "290S9N8=", "283S4N7=", "273S12N8=", "289S6N6=", "267S9N9=", "281S7N5=", "278S7N5=1X7=", "277S8N7=", "297S9N7=", "265S9N…
## $ j_cigar <chr> "288S11N32=1X4=", "318S7N12=1X15=", "305S5N6=1X14=1X21=", "321S15N5=1X23=1X17=", "290S17N19=", "296S26=1X21=", "311S11N4=1X33=", "280S2N17=1X6=1X21=", "299S8N4…
## $ v_sequence_start <int> 21, 21, 21, 21, 21, 21, 21, 20, 22, 21, 21, 20, 21, 21, 21, 21, 19, 21, 21, 21, 20, 21, 21, 21, 21, 21, 20, 23, 19, 21, 20, 21, 21, 20, 20, 21, 20, 22, 21, 21,…
## $ v_sequence_end <int> 269, 276, 283, 283, 283, 264, 283, 259, 281, 266, 264, 294, 258, 283, 273, 279, 274, 259, 278, 280, 262, 271, 281, 262, 264, 283, 259, 279, 278, 280, 261, 260,…
## $ v_germline_start <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
## $ v_germline_end <int> 320, 320, 320, 320, 320, 320, 320, 318, 318, 320, 320, 320, 319, 319, 317, 316, 316, 320, 318, 320, 320, 315, 318, 320, 321, 320, 318, 316, 320, 317, 319, 316,…
## $ d_sequence_start <int> 275, 306, 294, 291, 284, 274, 290, 268, 282, 279, 278, 298, 266, 292, 301, 285, 276, NA, 291, 284, 273, 279, 289, 277, 272, 299, 270, 292, 282, 295, 267, 265, …
## $ d_sequence_end <int> 281, 312, 305, 298, 290, 281, 295, 276, 286, 291, 284, 304, 273, 296, 307, 289, 282, NA, 297, 295, 293, 290, 294, 283, 287, 307, 280, 302, 290, 301, 280, 270, …
## $ d_germline_start <int> 6, 30, 14, 10, 5, 13, 7, 10, 8, 8, 9, 10, 10, 7, 22, 14, 4, NA, 24, 4, 2, 5, 8, 9, 6, 3, 1, 3, 7, 7, 4, 6, 11, 14, 12, 8, 2, 11, 8, 10, 5, 24, 4, 17, 5, 5, 4, …
## $ d_germline_end <int> 12, 36, 25, 17, 11, 20, 12, 18, 12, 20, 15, 16, 17, 11, 28, 18, 10, NA, 30, 15, 22, 16, 13, 15, 21, 11, 11, 13, 15, 13, 17, 11, 17, 18, 19, 13, 8, 16, 20, 16, …
## $ j_sequence_start <int> 289, 319, 306, 322, 291, 297, 312, 281, 300, 301, 289, 319, 276, 300, 317, 299, 296, 271, 336, 321, 303, 304, 300, 297, 293, 322, 289, 311, 315, 320, 283, 293,…
## $ j_sequence_end <int> 325, 346, 348, 368, 309, 344, 349, 326, 339, 347, 335, 361, 326, 334, 350, 333, 346, 320, 370, 338, 332, 338, 339, 333, 340, 368, 332, 345, 342, 362, 327, 327,…
## $ j_germline_start <int> 12, 8, 6, 16, 18, 1, 12, 3, 9, 2, 5, 20, 9, 14, 15, 14, 2, 13, 28, 18, 6, 14, 9, 15, 1, 16, 5, 14, 8, 5, 4, 12, 9, 1, 20, 15, 6, 6, 5, 6, 5, 9, 1, 6, 5, 5, 9, …
## $ j_germline_end <int> 48, 35, 48, 62, 36, 48, 49, 48, 48, 48, 51, 62, 59, 48, 48, 48, 52, 62, 62, 35, 35, 48, 48, 51, 48, 62, 48, 48, 35, 47, 48, 46, 48, 44, 62, 48, 48, 51, 50, 53,…
## $ junction_length <int> 36, 78, 45, 66, 33, 60, 48, 45, 36, 61, 51, 48, 51, 30, 54, 30, 48, 42, 71, 66, 78, 42, 36, 51, 57, 66, 51, 42, 72, 60, 45, 45, 45, 42, 36, 36, 57, 48, 51, 45,…
## $ np1_length <int> 5, 29, 10, 7, 0, 9, 6, 8, 0, 12, 13, 3, 7, 8, 27, 5, 1, 11, 12, 3, 10, 7, 7, 14, 7, 15, 10, 12, 3, 14, 5, 4, 4, 6, 1, 7, 1, 5, 4, 5, 26, 5, 0, 15, 26, 26, 8, 7…
## $ np2_length <int> 7, 6, 0, 23, 0, 15, 16, 4, 13, 9, 4, 14, 2, 3, 9, 9, 13, NA, 38, 25, 9, 13, 5, 13, 5, 14, 8, 8, 24, 18, 2, 22, 15, 3, 3, 11, 29, 11, 9, 5, 1, 5, 8, 0, 1, 1, 11…
## $ duplicate_count <int> 3, 3, 13, 3, 2, 2, 4, 2, 2, 2, 4, 2, 2, 2, 2, 2, 3, 3, 2, 2, 3, 2, 2, 2, 2, 2, 2, 5, 2, 2, 3, 2, 4, 2, 3, 4, 8, 2, 2, 2, 2, 3, 2, 4, 3, 4, 2, 5, 2, 2, 7, 3, 2,…
## $ sequence_id <chr> "SRR765688.7787", "SRR765688.35420", "SRR765688.36681", "SRR765688.33811", "SRR765688.44149", "SRR765688.15636", "SRR765688.20304", "SRR765688.13860", "SRR7…
## $ sequence <chr> "NNNNNNNNNNNNNNNNNNNNGCTGACCTGCACCTTCTCTGGATTCTCACTCAGTACTAGTGCAGTGGGTGTACACTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGCCAAATATTACAGCACCAG…
## $ rev_comp <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FA…
## $ productive <lgl> TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, FALSE, TRUE, FALSE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, T…
## $ vj_in_frame <lgl> TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE…
## $ stop_codon <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, …
## $ v_call <chr> "IGHV2-5*02", "IGHV5-51*01", "IGHV7-4-1*02", "IGHV7-4-1*02", "IGHV7-4-1*02", "IGHV2-5*02", "IGHV7-4-1*02", "IGHV6-1*01,IGHV6-1*02", "IGHV7-4-1*02", "IGHV4-3…
## $ d_call <chr> "IGHD5-24*01", "IGHD3-16*02,IGHD3-3*01,IGHD3-3*02", "IGHD3-22*01", "IGHD3-9*01", "IGHD1-26*01", "IGHD2-21*02", "IGHD1-26*01,IGHD2-21*02,IGHD3/OR15-3a*01", "…
## $ j_call <chr> "IGHJ4*02", "IGHJ6*02,IGHJ6*04", "IGHJ4*02", "IGHJ6*02", "IGHJ6*01", "IGHJ4*02", "IGHJ5*02", "IGHJ4*02", "IGHJ4*02", "IGHJ4*02", "IGHJ5*02", "IGHJ6*02", "IG…
## $ c_call <chr> "IGHG", "IGHG", "IGHG", "IGHG", "IGHG", "IGHA", "IGHA", "IGHG", "IGHG", "IGHA", "IGHA", "IGHG", "IGHA", "IGHA", "IGHG", "IGHA", "IGHG", "IGHA", "IGHG", "IGH…
## $ sequence_alignment <chr> "...........................................................GCTGACCTGCACCTTCTCTGGATTCTCACTCAGT......ACTAGTGCAGTGGGTGTACACTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTG…
## $ germline_alignment <chr> "CAGATCACCTTGAAGGAGTCTGGTCCT...ACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGC......ACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTG…
## $ junction <chr> "TGTGCACACAGTGCGGGATGGCTGCCTGATTACTGG", "TGTGCGAGGCATGGATTATACGGTTGTGATCATACCGGCTGTTATACAAGCTTCTACTACTACGGGATGGACGTCTGG", "TGTGCGAGAGAAGAACGTCGAAGTAGTGGTTAT…
## $ junction_aa <chr> "CAHSAGWLPDYW", "CARHGLYGCDHTGCYTSFYYYGMDVW", "CAREERRSSGYFDHW", "CAREGYYFDTTGSPRSHGLDVW", "CARDSGGMDVW", "CVLSRRLGDSGVQKYYFDYW", "CAREGLWDGRVVTDLW", "CARTR…
## $ v_cigar <chr> "20S56N21=1X11=1X7=1X9=3X62=6D2=1X1=2X2=2X50=1X7=1X4=1X22=1X30=", "20S40N15=1X15=1X11=1X2=1X1=1X1=2X3=1X7=1X41=2X2=1X10=1X3=1X1=1X5=2X5=1X4=1X9=1X19=1X24=2X…
## $ d_cigar <chr> "274S5N7=", "305S29N7=", "293S13N12=", "290S9N8=", "283S4N7=", "273S12N8=", "289S6N6=", "267S9N9=", "281S7N5=", "278S7N5=1X7=", "277S8N7=", "297S9N7=", "265…
## $ j_cigar <chr> "288S11N32=1X4=", "318S7N12=1X15=", "305S5N6=1X14=1X21=", "321S15N5=1X23=1X17=", "290S17N19=", "296S26=1X21=", "311S11N4=1X33=", "280S2N17=1X6=1X21=", "299S…
## $ v_sequence_start <int> 21, 21, 21, 21, 21, 21, 21, 20, 22, 21, 21, 20, 21, 21, 21, 21, 19, 21, 21, 21, 20, 21, 21, 21, 21, 21, 20, 23, 19, 21, 20, 21, 21, 20, 20, 21, 20, 22, 21, …
## $ v_sequence_end <int> 269, 276, 283, 283, 283, 264, 283, 259, 281, 266, 264, 294, 258, 283, 273, 279, 274, 259, 278, 280, 262, 271, 281, 262, 264, 283, 259, 279, 278, 280, 261, 2…
## $ v_germline_start <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, …
## $ v_germline_end <int> 320, 320, 320, 320, 320, 320, 320, 318, 318, 320, 320, 320, 319, 319, 317, 316, 316, 320, 318, 320, 320, 315, 318, 320, 321, 320, 318, 316, 320, 317, 319, 3…
## $ d_sequence_start <int> 275, 306, 294, 291, 284, 274, 290, 268, 282, 279, 278, 298, 266, 292, 301, 285, 276, NA, 291, 284, 273, 279, 289, 277, 272, 299, 270, 292, 282, 295, 267, 26…
## $ d_sequence_end <int> 281, 312, 305, 298, 290, 281, 295, 276, 286, 291, 284, 304, 273, 296, 307, 289, 282, NA, 297, 295, 293, 290, 294, 283, 287, 307, 280, 302, 290, 301, 280, 27…
## $ d_germline_start <int> 6, 30, 14, 10, 5, 13, 7, 10, 8, 8, 9, 10, 10, 7, 22, 14, 4, NA, 24, 4, 2, 5, 8, 9, 6, 3, 1, 3, 7, 7, 4, 6, 11, 14, 12, 8, 2, 11, 8, 10, 5, 24, 4, 17, 5, 5, …
## $ d_germline_end <int> 12, 36, 25, 17, 11, 20, 12, 18, 12, 20, 15, 16, 17, 11, 28, 18, 10, NA, 30, 15, 22, 16, 13, 15, 21, 11, 11, 13, 15, 13, 17, 11, 17, 18, 19, 13, 8, 16, 20, 1…
## $ j_sequence_start <int> 289, 319, 306, 322, 291, 297, 312, 281, 300, 301, 289, 319, 276, 300, 317, 299, 296, 271, 336, 321, 303, 304, 300, 297, 293, 322, 289, 311, 315, 320, 283, 2…
## $ j_sequence_end <int> 325, 346, 348, 368, 309, 344, 349, 326, 339, 347, 335, 361, 326, 334, 350, 333, 346, 320, 370, 338, 332, 338, 339, 333, 340, 368, 332, 345, 342, 362, 327, 3…
## $ j_germline_start <int> 12, 8, 6, 16, 18, 1, 12, 3, 9, 2, 5, 20, 9, 14, 15, 14, 2, 13, 28, 18, 6, 14, 9, 15, 1, 16, 5, 14, 8, 5, 4, 12, 9, 1, 20, 15, 6, 6, 5, 6, 5, 9, 1, 6, 5, 5, …
## $ j_germline_end <int> 48, 35, 48, 62, 36, 48, 49, 48, 48, 48, 51, 62, 59, 48, 48, 48, 52, 62, 62, 35, 35, 48, 48, 51, 48, 62, 48, 48, 35, 47, 48, 46, 48, 44, 62, 48, 48, 51, 50, …
## $ junction_length <int> 36, 78, 45, 66, 33, 60, 48, 45, 36, 61, 51, 48, 51, 30, 54, 30, 48, 42, 71, 66, 78, 42, 36, 51, 57, 66, 51, 42, 72, 60, 45, 45, 45, 42, 36, 36, 57, 48, 51, …
## $ np1_length <int> 5, 29, 10, 7, 0, 9, 6, 8, 0, 12, 13, 3, 7, 8, 27, 5, 1, 11, 12, 3, 10, 7, 7, 14, 7, 15, 10, 12, 3, 14, 5, 4, 4, 6, 1, 7, 1, 5, 4, 5, 26, 5, 0, 15, 26, 26, 8…
## $ np2_length <int> 7, 6, 0, 23, 0, 15, 16, 4, 13, 9, 4, 14, 2, 3, 9, 9, 13, NA, 38, 25, 9, 13, 5, 13, 5, 14, 8, 8, 24, 18, 2, 22, 15, 3, 3, 11, 29, 11, 9, 5, 1, 5, 8, 0, 1, 1,…
## $ duplicate_count <int> 3, 3, 13, 3, 2, 2, 4, 2, 2, 2, 4, 2, 2, 2, 2, 2, 3, 3, 2, 2, 3, 2, 2, 2, 2, 2, 2, 5, 2, 2, 3, 2, 4, 2, 3, 4, 8, 2, 2, 2, 2, 3, 2, 4, 3, 4, 2, 5, 2, 2, 7, 3,…

Reading AIRR Data Models
~~~~~~~~~~~~~~~~~~~~~~~~
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61 changes: 58 additions & 3 deletions docs/standards/news.rst
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Schema Release Notes
================================================================================

Version 1.4.2: TBD, 2023
Version 1.5.0: August 31, 2023
--------------------------------------------------------------------------------

1. Added "IGI" to all locus enum fields.
**Version 1.5 schema release.**

General Schema Changes:

1. Fixed synchronization errors between the OpenAPI v2 and v3 versions of the
AIRR Schema (airr-schema.yaml and airr-schema-openapi3.yaml).
2. Set the default value of ``x-airr.miarr`` attributes to ``defined``.
3. Converted all ``x-airr.format`` attribute values to snake_case, which
specifically impacts any instance of ``controlled vocabulary`` or
``physical quantity``.
4. Corrected numerous instances of missing `x-airr.miairr` and
`x-airr.identifier` attributes.
5. Replaced ``x-airr.adc-api-optional`` attribute with
``x-airr.adc-query-support`` in multiple fields.
6. Added "IGI" as a valid value to the ``locus`` enum fields in multiple
schema.
7. Added ``null`` as a valide value to all nullable enum fields.
8. Removed ``discriminator: AIRR`` from all object definitions.

Germline and Genotype Schema:

1. Clarified the descriptions of multiple fields in the Germline and
Genotype schema.
2. Modified ``x-airr: nullable`` and ``x-airr: identifier`` values on multiple
Germline schema.
fields in the Germline and Genotype schema.
3. Removed the ``alignment`` field and added the ``unaligned_sequence``,
``aligned_sequences``, and ``alignment_labels`` fields to the
``SequenceDelineationV`` object.
4. Converted the enum values in the ``inference_type`` field of
``AlleleDescription`` to snake_case.
5. Added the ``allele_similarity_cluster_designation`` and
``allele_similarity_cluster_member_id`` fields to ``AlleleDescription``.
6. Moved the nested objects ``DocumentedAllele``, ``UndocumentedAllele``, and
``DeletedGenes`` out of ``Genotype`` and defined them as top-level objects
references by the ``documented_alleles``, ``undocumented_alleles``, and
``deleted_genes`` fields, respectively.
7. Moved the nested object ``MHCAllele`` out of ``MHCGenotype`` and defined
it as a top-level object referenced by the ``mhc_alleles`` field.

Single-cell Schema:

1. Added the ``property_type`` field to the ``CellExpression`` object.
2. Moved the nested ``ReceptorReactivity`` object out of ``Receptor``
and defined it as a top-level object referenced by the
``reactivity_measurements`` field.

Subject Schema:

1. Removed the nested references to ``GenotypeSet`` and ``MHCGenotypeSet``
in the ``genotype`` field and modified the definition to point to a
top-level ``SubjectGenotype`` object defining these references.

DataProcessing Schema:

1. Clarified the description of ``quality_thresholds`` to indicate that
quality filtering is not mandatory.



Version 1.4.1: August 27, 2022
--------------------------------------------------------------------------------
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Package: airr
Type: Package
Version: 1.4.1
Date: 2022-08-27
Version: 1.5.0
Date: 2023-08-28
Authors@R: c(person("Jason", "Vander Heiden", role=c("aut", "cre"),
email="[email protected]"),
person("Susanna", "Marquez", role=c("aut"),
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rmarkdown,
tibble,
testthat
RoxygenNote: 7.2.1
RoxygenNote: 7.2.3
6 changes: 6 additions & 0 deletions lang/R/NEWS.md
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Version 1.5.0: August 28, 2023
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+ Updated schema set and examples to v1.5.


Version 1.4.1: August 27, 2022
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2 changes: 1 addition & 1 deletion lang/R/docs/build.R
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Original file line number Diff line number Diff line change
Expand Up @@ -6,5 +6,5 @@ build_mkdocs(".", doc_path=doc_path, style="sphinx", yaml=F)
run_pandoc(doc_path, format="rst", delete=T)

# TODO: Post execution we still need to do cleanup:
# Edit the title and about in docs/packages/airr-R/overview.rst
# Edit the title and about in docs/packages/airr-R/overview.rst and about.rst
# Remove the progress bar from the example in docs/*_tabular.rst and docs/ExampleData.rst
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