pav3 3.0.0.dev23__tar.gz → 3.0.0.dev26__tar.gz

{pav3-3.0.0.dev23 → pav3-3.0.0.dev26}/CONTRIBUTING.md

@@ -5,7 +5,7 @@ features.
 
 ## Bugs, questions, and feature requests
 
-The project's [GitHub issues page](https://github.com/BeckLaboratory/pav/issues) may be used to ask questions,
+The project's [GitHub issues page](https://github.com/BeckLaboratory/pav3/issues) may be used to ask questions,
 report bugs, and request features.
 
 Please search for related issues before opening a new one. If you find a relevant open issue, you may monitor it for
@@ -49,7 +49,7 @@ Please make sure you understand the [Code of Conduct](CODE_OF_CONDUCT.md) before
 
 Pull the codebase from GitHub:
 ```bash
-git clone https://github.com/BeckLaboratory/pav.git
+git clone https://github.com/BeckLaboratory/pav3.git
 cd pav
 ```
 

{pav3-3.0.0.dev23/src/pav3.egg-info → pav3-3.0.0.dev26}/PKG-INFO

@@ -1,17 +1,32 @@
 Metadata-Version: 2.4
 Name: pav3
-Version: 3.0.0.dev23
+Version: 3.0.0.dev26
 Summary: Assembly-based variant discovery
+Author-email: Peter Audano <peter.audano@jax.org>
+Maintainer-email: Peter Audano <peter.audano@jax.org>
 License-Expression: MIT
+Project-URL: Homepage, https://github.com/BeckLaboratory/pav3
+Project-URL: Documentation, https://pav3.readthedocs.io
+Project-URL: Repository, https://github.com/BeckLaboratory/pav3
+Project-URL: Issues, https://github.com/BeckLaboratory/pav3/issues
+Project-URL: Changelog, https://github.com/BeckLaboratory/pav3/blob/main/CHANGELOG.md
+Keywords: variant calling,variant discovery,assembly-based,long-read,bioinformatics,genomics
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: agglovar==0.0.1.dev14
+Requires-Dist: agglovar>=0.0.1.dev18
 Requires-Dist: biopython>=1.85
 Requires-Dist: fastexcel>=0.14.0
 Requires-Dist: frozendict>=2.4.6
 Requires-Dist: hmmlearn>=0.3.3
 Requires-Dist: intervaltree>=3.1.0
+Requires-Dist: matplotlib>=3.11.0
 Requires-Dist: numpy>=2.3.2
 Requires-Dist: polars[numpy,pandas,pyarrow]>=1.41.0
 Requires-Dist: pyarrow>=21.0.0
@@ -19,8 +34,7 @@ Requires-Dist: pysam>=0.23.3
 Requires-Dist: scipy>=1.16.1
 Requires-Dist: scipy-stubs==1.16.1.1
 Requires-Dist: snakemake>=9.9.0
-Provides-Extra: fig
-Requires-Dist: matplotlib>=3.10.8; extra == "fig"
+Requires-Dist: xlsxwriter>=3.2.9
 Dynamic: license-file
 
 <h1 align="center"><img width="300px" src="img/logo/PAVLogo_Full.png"/></h1>
@@ -31,40 +45,23 @@ Dynamic: license-file
 
 Variant caller for assembled genomes.
 
-Please discuss with authors prior to publishing results using PAV 3. A paper describing PAV 3 is in
-preparation and is expected mid-2026.
-
-## Development release (Please read)
-
-PAV 3 is currently a development release and may contain bugs. Please report problems you encounter.
-
-PAV now uses Polars for fast data manipulation. If your job fails with strange Polars errors, such as "capacity
-overflow" or "PanicException", this is likely from Polars running out of memory.
-
-
-### Notes for early adopters
-
-If you have been using development versions, please read about these changes.
-
-**Call subcommand is deprecated.** If you have been running pav3 with the "call" subcommand, switch it to "batch"
-(i.e. ("pav3 batch ...")). A future version will use "call" for single assemblies (with multiple haplotypes) defined on
-the command-line and "batch" to run all assemblies from an assembly table.
-
-**Moving configuration to pav.json.** The configuration file "config.json" is being moved to "pav.json". A future
-version will ignore "config.json".
+Please discuss with authors prior to publishing results using PAV 3; contact
+[contact information](https://www.jax.org/people/peter-audano). A paper describing PAV 3 is in
+preparation.
 
 
 ## Install and run
 
 
 ### Install
+PAV requires Python 3.12 or newer.
 ```
 pip install pav3
 ```
 
 ### Run
-To run PAV, use the `pav3 batch` command after setting up configuration files (see below). A future version will add
-`pav call` for single-assemblies without requiring configuration files. 
+To run PAV, use the `pav3 batch` command after setting up configuration files (see below). A future version may add
+a command for single-assemblies without requiring configuration files.
 
 Some Python environments may require you to run `pav3` through the `python` command:
 ```
@@ -72,13 +69,45 @@ python -m pav3 batch
 ```
 
 
+### Containers
+
+Public container images include PAV and all dependencies.
+
+> [!IMPORTANT]
+> Pulling containers will generate 401 errors pending permissions changes by our organization. This should be
+> corrected within a few days, please check back.
+
+Docker:
+```
+docker pull ghcr.io/becklaboratory/pav3:latest
+
+docker run --rm -v "$PWD:$PWD" -w "$PWD" --user "$(id -u):$(id -g)" \
+    ghcr.io/becklaboratory/pav3:latest batch
+```
+
+Apptainer (or Singularity):
+```
+apptainer pull pav3.sif oras://ghcr.io/becklaboratory/pav3-sif:latest
+
+apptainer run pav3.sif batch
+```
+
+The container runs `pav3` itself, so arguments follow the image exactly as they would on the command line (`batch`,
+`--help`, and so on).
+
+Both examples give PAV access to the current directory only. If the reference genome or the assemblies are somewhere
+else, make those locations visible as well: add `-v /path:/path` for Docker or `--bind /path` for Apptainer.
+
+Replace `latest` with a version (e.g. `3.0.0.dev24`) to pin a specific release.
+
+
 ### Dependencies
-Currently, PAV needs `minimap2` in the environment where it is run. This may change in future releases. All other
-dependencies are handled by the installer.
+Currently, PAV needs `minimap2` in the environment where it is run (the containers above already include it). This may
+change in future releases. All other dependencies are handled by the installer.
 
 
 ### Output
-PAV will output a VCF file for each sample called `NAME.vcf.gz`.
+PAV will output a VCF file `NAME.vcf.gz` to the run directory for each sample.
 
 * `results/NAME/call_hap`: Unmerged variant calls.
   * Includes tables of callable regions in reference ("callable_ref") and query ("callable_qry") coordinates.
@@ -113,61 +142,67 @@ The assembly table points PAV to input assemblies. It may be in TSV, CSV, Excel,
 optionally be gzipped). Each assembly has one row in the table.
 
 Columns:
-* NAME: Assembly or sample name.
-* HAP_\*: One column for each assembled haplotype.
+* name: Assembly or sample name.
+* hap_\*: One column for each assembled haplotype.
 
 
 #### Name column
 
-The `NAME` column contains the assembly name (or sample name). This column must be present and each row must have a
+The `name` column contains the assembly name (or sample name). This column must be present and each row must have a
 unique value.
 
 
 #### Haplotype columns
 
-PAV accepts one or more assembled haplotypes per assembly, each with a column in the table starting with "HAP_". Each
+PAV accepts one or more assembled haplotypes per assembly, each with a column in the table starting with "hap_". Each
 is a path to an input file for one assembly haplotype.
 
-Common column names are "HAP_h1" for haplotype "h1" and "HAP_h2" for haplotype "h2". For some assemblies with known
-parental origins, "HAP_mat" and "HAP_pat" are commonly used.
+Common column names are "hap_h1" for haplotype "h1" and "hap_h2" for haplotype "h2". For some assemblies with known
+parental origins, "hap_pat" and "hap_mat" are commonly used.
 
 There must be at least one haplotype per assembly, and PAV has no limits on the number of haplotypes (i.e. 3 or more
 are acceptable).
 
-Not all assemblies need to have the same haplotypes. PAV will ignore empty the "HAP_" values for each assembly. For
-example, if some assemblies have an "unphased" haplotype and other do not, include "HAP_unphased" and leave it blank
-for assemblies that do not have it.
+Not all assemblies need to have the same haplotypes. PAV will ignore empty "hap_" values for each assembly where the
+path is empty. For example, if some assemblies have an "unphased" haplotype and others do not, include the
+"hap_unphased" column and leave it blank for assemblies that do not have it.
 
 Note that genotypes in the VCF file will have one allele for each haplotype defined for the assembly. For an assembly
 with haplotypes "h1", "h2", and "unphased", three genotype alleles will be possible (e.g. "1|0|." for a heterozygous
 variant present in "h1", not present in "h2", and uncallable in "unphased"). The order of genotypes is determined by
 the order of haplotype columns in the assembly table.
 
-Each "HAP_" column contains paths to input files in FASTA, FASTQ, GFA, or FOFN format. FOFN may contain paths to these
+Each "hap_" column contains paths to input files in FASTA, FASTQ, GFA, or FOFN format. FOFN may contain paths to these
 same file types including other FOFNs (recursive FOFNs are not recommended, but PAV will detect cycles). Multiple files
 can be input by separating them by semi-colons (i.e. "path/to/file1.fasta.gz;path/to/file2.fasta.gz") and a mix of
-types is possible. PAV will be fastest if the input is a single bgzipped and indexed FASTA file, it will build its
-own FASTA file for all other cases.
+types is possible.
+
+PAV will be fastest if the input is a single indexed FASTA file, which may be plain text or bgzipped (Samtools bgzip).
+For all other input including multiple FASTA files or any GFA files for one haplotype, PAV will build a single FASTA
+file from the input, index it, and use it for variant calling.
 
 
 #### Configuration column for global overrides
 
-An optional "CONFIG" column can override global configuration parameters per assembly. Global configuration parameters
+An optional "config" column can override global configuration parameters per assembly. Global configuration parameters
 are defined in `pav.json` or are PAV default values if not defined. Values in this column are semicolon-separated lists
-of key-value pairs (i.e. "key1=val1;key2=val2"). The "reference" parameter cannot be overridden per assembly.
+of key-value pairs (i.e. "key1=val1;key2=val2"). The "reference" parameter cannot be set in the assembly table.
 
 
-### A note on references
+### Suitable genome references
 
-Do not use references with ALT, PATCH, or DECOY scaffolds for PAV, or generally, any assembly-based or long-read
-variant calling tool. Reference redundancy may increase callset errors.
+Align against primary assemblies composed of chromosome scaffolds including unplaced contigs and unlocalized contigs
+if they exist (GRCh/hg references). Do not use references with ALT, PATCH, or DECOY scaffolds. Reference redundancy
+from these non-primary contigs may increase callset errors.
 
-The GRCh38 HGSVC no-ALT reference for long reads can be found here:
-ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC2/technical/reference/20200513_hg38_NoALT/
+The GRCh38 HGSVC no-ALT reference for long reads was shared by the HGSVC consortium:
+https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC2/technical/reference/20200513_hg38_NoALT/
 
-The T2T-CHM13v2.0 (hs1 on UCSC) is suitable without alteration. Custom per-sample assemblies containing a
-single-haplotype or an unphased ("squashed") assembly typically also make a suitable reference as long as they are
-free of large structural misassemblies and especially large false duplications.
+The T2T-CHM13v2.0 (hs1 on UCSC) is suitable without alteration.
+
+Custom per-sample assemblies containing a single-haplotype or an unphased ("squashed") assembly typically also make a
+suitable reference as long as they are free of large structural misassemblies and large false duplications. For phased
+assemblies, choose only one haplotype as a reference.
 
 
 ## PAV versions
@@ -176,8 +211,8 @@ PAV uses Python package versioning with three fields:
 
 * Major: Major changes or new features.
 * Minor: Small changes, but may affect PAV's API or command-line interfaces.
-* Patch: Small changes and minor new features. Patch versions do break API or command-line compatibility, but may
-  add minor features or options to the API that were not previously supported.
+* Patch: Small changes and minor new features. Patch versions do not break API or command-line compatibility, but may
+  add new features.
 
 PAV follows Python's packaging versioning scheme (https://packaging.python.org/en/latest/discussions/versioning/).
 
@@ -187,9 +222,20 @@ and "3.0.0a1" is an early alpha version, and "3.0.0rc1" is a release candidate,
 release and should not be considered production-ready.
 
 
+## Reporting bugs
+
+Please report problems you encounter on the
+[issues page](https://github.com/BeckLaboratory/pav3/issues).
+
+
 ## Cite PAV
 
 PAV 3 does not yet have a citation. For now, use the citation for previous PAV versions, but check back for updates.
 
 Ebert et al., “Haplotype-Resolved Diverse Human Genomes and Integrated Analysis of Structural Variation,”
 Science, February 25, 2021, eabf7117, https://doi.org/10.1126/science.abf7117 (PMID: 33632895).
+
+
+## License
+
+PAV is released under the MIT License. See [LICENSE](LICENSE).

pav3-3.0.0.dev23/PKG-INFO → pav3-3.0.0.dev26/README.md

@@ -1,28 +1,3 @@
-Metadata-Version: 2.4
-Name: pav3
-Version: 3.0.0.dev23
-Summary: Assembly-based variant discovery
-License-Expression: MIT
-Requires-Python: >=3.12
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: agglovar==0.0.1.dev14
-Requires-Dist: biopython>=1.85
-Requires-Dist: fastexcel>=0.14.0
-Requires-Dist: frozendict>=2.4.6
-Requires-Dist: hmmlearn>=0.3.3
-Requires-Dist: intervaltree>=3.1.0
-Requires-Dist: numpy>=2.3.2
-Requires-Dist: polars[numpy,pandas,pyarrow]>=1.41.0
-Requires-Dist: pyarrow>=21.0.0
-Requires-Dist: pysam>=0.23.3
-Requires-Dist: scipy>=1.16.1
-Requires-Dist: scipy-stubs==1.16.1.1
-Requires-Dist: snakemake>=9.9.0
-Provides-Extra: fig
-Requires-Dist: matplotlib>=3.10.8; extra == "fig"
-Dynamic: license-file
-
 <h1 align="center"><img width="300px" src="img/logo/PAVLogo_Full.png"/></h1>
 <p align="center">Phased Assembly Variant Caller</p>
 
@@ -31,40 +6,23 @@ Dynamic: license-file
 
 Variant caller for assembled genomes.
 
-Please discuss with authors prior to publishing results using PAV 3. A paper describing PAV 3 is in
-preparation and is expected mid-2026.
-
-## Development release (Please read)
-
-PAV 3 is currently a development release and may contain bugs. Please report problems you encounter.
-
-PAV now uses Polars for fast data manipulation. If your job fails with strange Polars errors, such as "capacity
-overflow" or "PanicException", this is likely from Polars running out of memory.
-
-
-### Notes for early adopters
-
-If you have been using development versions, please read about these changes.
-
-**Call subcommand is deprecated.** If you have been running pav3 with the "call" subcommand, switch it to "batch"
-(i.e. ("pav3 batch ...")). A future version will use "call" for single assemblies (with multiple haplotypes) defined on
-the command-line and "batch" to run all assemblies from an assembly table.
-
-**Moving configuration to pav.json.** The configuration file "config.json" is being moved to "pav.json". A future
-version will ignore "config.json".
+Please discuss with authors prior to publishing results using PAV 3; contact
+[contact information](https://www.jax.org/people/peter-audano). A paper describing PAV 3 is in
+preparation.
 
 
 ## Install and run
 
 
 ### Install
+PAV requires Python 3.12 or newer.
 ```
 pip install pav3
 ```
 
 ### Run
-To run PAV, use the `pav3 batch` command after setting up configuration files (see below). A future version will add
-`pav call` for single-assemblies without requiring configuration files. 
+To run PAV, use the `pav3 batch` command after setting up configuration files (see below). A future version may add
+a command for single-assemblies without requiring configuration files.
 
 Some Python environments may require you to run `pav3` through the `python` command:
 ```
@@ -72,13 +30,45 @@ python -m pav3 batch
 ```
 
 
+### Containers
+
+Public container images include PAV and all dependencies.
+
+> [!IMPORTANT]
+> Pulling containers will generate 401 errors pending permissions changes by our organization. This should be
+> corrected within a few days, please check back.
+
+Docker:
+```
+docker pull ghcr.io/becklaboratory/pav3:latest
+
+docker run --rm -v "$PWD:$PWD" -w "$PWD" --user "$(id -u):$(id -g)" \
+    ghcr.io/becklaboratory/pav3:latest batch
+```
+
+Apptainer (or Singularity):
+```
+apptainer pull pav3.sif oras://ghcr.io/becklaboratory/pav3-sif:latest
+
+apptainer run pav3.sif batch
+```
+
+The container runs `pav3` itself, so arguments follow the image exactly as they would on the command line (`batch`,
+`--help`, and so on).
+
+Both examples give PAV access to the current directory only. If the reference genome or the assemblies are somewhere
+else, make those locations visible as well: add `-v /path:/path` for Docker or `--bind /path` for Apptainer.
+
+Replace `latest` with a version (e.g. `3.0.0.dev24`) to pin a specific release.
+
+
 ### Dependencies
-Currently, PAV needs `minimap2` in the environment where it is run. This may change in future releases. All other
-dependencies are handled by the installer.
+Currently, PAV needs `minimap2` in the environment where it is run (the containers above already include it). This may
+change in future releases. All other dependencies are handled by the installer.
 
 
 ### Output
-PAV will output a VCF file for each sample called `NAME.vcf.gz`.
+PAV will output a VCF file `NAME.vcf.gz` to the run directory for each sample.
 
 * `results/NAME/call_hap`: Unmerged variant calls.
   * Includes tables of callable regions in reference ("callable_ref") and query ("callable_qry") coordinates.
@@ -113,61 +103,67 @@ The assembly table points PAV to input assemblies. It may be in TSV, CSV, Excel,
 optionally be gzipped). Each assembly has one row in the table.
 
 Columns:
-* NAME: Assembly or sample name.
-* HAP_\*: One column for each assembled haplotype.
+* name: Assembly or sample name.
+* hap_\*: One column for each assembled haplotype.
 
 
 #### Name column
 
-The `NAME` column contains the assembly name (or sample name). This column must be present and each row must have a
+The `name` column contains the assembly name (or sample name). This column must be present and each row must have a
 unique value.
 
 
 #### Haplotype columns
 
-PAV accepts one or more assembled haplotypes per assembly, each with a column in the table starting with "HAP_". Each
+PAV accepts one or more assembled haplotypes per assembly, each with a column in the table starting with "hap_". Each
 is a path to an input file for one assembly haplotype.
 
-Common column names are "HAP_h1" for haplotype "h1" and "HAP_h2" for haplotype "h2". For some assemblies with known
-parental origins, "HAP_mat" and "HAP_pat" are commonly used.
+Common column names are "hap_h1" for haplotype "h1" and "hap_h2" for haplotype "h2". For some assemblies with known
+parental origins, "hap_pat" and "hap_mat" are commonly used.
 
 There must be at least one haplotype per assembly, and PAV has no limits on the number of haplotypes (i.e. 3 or more
 are acceptable).
 
-Not all assemblies need to have the same haplotypes. PAV will ignore empty the "HAP_" values for each assembly. For
-example, if some assemblies have an "unphased" haplotype and other do not, include "HAP_unphased" and leave it blank
-for assemblies that do not have it.
+Not all assemblies need to have the same haplotypes. PAV will ignore empty "hap_" values for each assembly where the
+path is empty. For example, if some assemblies have an "unphased" haplotype and others do not, include the
+"hap_unphased" column and leave it blank for assemblies that do not have it.
 
 Note that genotypes in the VCF file will have one allele for each haplotype defined for the assembly. For an assembly
 with haplotypes "h1", "h2", and "unphased", three genotype alleles will be possible (e.g. "1|0|." for a heterozygous
 variant present in "h1", not present in "h2", and uncallable in "unphased"). The order of genotypes is determined by
 the order of haplotype columns in the assembly table.
 
-Each "HAP_" column contains paths to input files in FASTA, FASTQ, GFA, or FOFN format. FOFN may contain paths to these
+Each "hap_" column contains paths to input files in FASTA, FASTQ, GFA, or FOFN format. FOFN may contain paths to these
 same file types including other FOFNs (recursive FOFNs are not recommended, but PAV will detect cycles). Multiple files
 can be input by separating them by semi-colons (i.e. "path/to/file1.fasta.gz;path/to/file2.fasta.gz") and a mix of
-types is possible. PAV will be fastest if the input is a single bgzipped and indexed FASTA file, it will build its
-own FASTA file for all other cases.
+types is possible.
+
+PAV will be fastest if the input is a single indexed FASTA file, which may be plain text or bgzipped (Samtools bgzip).
+For all other input including multiple FASTA files or any GFA files for one haplotype, PAV will build a single FASTA
+file from the input, index it, and use it for variant calling.
 
 
 #### Configuration column for global overrides
 
-An optional "CONFIG" column can override global configuration parameters per assembly. Global configuration parameters
+An optional "config" column can override global configuration parameters per assembly. Global configuration parameters
 are defined in `pav.json` or are PAV default values if not defined. Values in this column are semicolon-separated lists
-of key-value pairs (i.e. "key1=val1;key2=val2"). The "reference" parameter cannot be overridden per assembly.
+of key-value pairs (i.e. "key1=val1;key2=val2"). The "reference" parameter cannot be set in the assembly table.
+
 
+### Suitable genome references
 
-### A note on references
+Align against primary assemblies composed of chromosome scaffolds including unplaced contigs and unlocalized contigs
+if they exist (GRCh/hg references). Do not use references with ALT, PATCH, or DECOY scaffolds. Reference redundancy
+from these non-primary contigs may increase callset errors.
 
-Do not use references with ALT, PATCH, or DECOY scaffolds for PAV, or generally, any assembly-based or long-read
-variant calling tool. Reference redundancy may increase callset errors.
+The GRCh38 HGSVC no-ALT reference for long reads was shared by the HGSVC consortium:
+https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC2/technical/reference/20200513_hg38_NoALT/
 
-The GRCh38 HGSVC no-ALT reference for long reads can be found here:
-ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC2/technical/reference/20200513_hg38_NoALT/
+The T2T-CHM13v2.0 (hs1 on UCSC) is suitable without alteration.
 
-The T2T-CHM13v2.0 (hs1 on UCSC) is suitable without alteration. Custom per-sample assemblies containing a
-single-haplotype or an unphased ("squashed") assembly typically also make a suitable reference as long as they are
-free of large structural misassemblies and especially large false duplications.
+Custom per-sample assemblies containing a single-haplotype or an unphased ("squashed") assembly typically also make a
+suitable reference as long as they are free of large structural misassemblies and large false duplications. For phased
+assemblies, choose only one haplotype as a reference.
 
 
 ## PAV versions
@@ -176,8 +172,8 @@ PAV uses Python package versioning with three fields:
 
 * Major: Major changes or new features.
 * Minor: Small changes, but may affect PAV's API or command-line interfaces.
-* Patch: Small changes and minor new features. Patch versions do break API or command-line compatibility, but may
-  add minor features or options to the API that were not previously supported.
+* Patch: Small changes and minor new features. Patch versions do not break API or command-line compatibility, but may
+  add new features.
 
 PAV follows Python's packaging versioning scheme (https://packaging.python.org/en/latest/discussions/versioning/).
 
@@ -187,9 +183,20 @@ and "3.0.0a1" is an early alpha version, and "3.0.0rc1" is a release candidate,
 release and should not be considered production-ready.
 
 
+## Reporting bugs
+
+Please report problems you encounter on the
+[issues page](https://github.com/BeckLaboratory/pav3/issues).
+
+
 ## Cite PAV
 
 PAV 3 does not yet have a citation. For now, use the citation for previous PAV versions, but check back for updates.
 
 Ebert et al., “Haplotype-Resolved Diverse Human Genomes and Integrated Analysis of Structural Variation,”
 Science, February 25, 2021, eabf7117, https://doi.org/10.1126/science.abf7117 (PMID: 33632895).
+
+
+## License
+
+PAV is released under the MIT License. See [LICENSE](LICENSE).

{pav3-3.0.0.dev23 → pav3-3.0.0.dev26}/pyproject.toml

@@ -11,12 +11,13 @@ readme = "README.md"
 
 requires-python = ">=3.12"
 dependencies = [
-    "agglovar==0.0.1.dev14",
+    "agglovar>=0.0.1.dev18",
     "biopython>=1.85",
     "fastexcel>=0.14.0",
     "frozendict>=2.4.6",
     "hmmlearn>=0.3.3",
     "intervaltree>=3.1.0",
+    "matplotlib>=3.11.0",
     "numpy>=2.3.2",
     "polars[numpy,pandas,pyarrow]>=1.41.0",
     "pyarrow>=21.0.0",
@@ -24,23 +25,9 @@ dependencies = [
     "scipy>=1.16.1",
     "scipy-stubs==1.16.1.1",
     "snakemake>=9.9.0",
+    "xlsxwriter>=3.2.9",
 ]
 
-[project.scripts]
-pav3 = "pav3.cli:main"
-
-[project.optional-dependencies]
-fig = [
-    "matplotlib>=3.10.8",
-]
-
-[pav.urls]
-Homepage = "https://github.com/BeckLaboratory/pav"
-Documentation = "https://pav3.readthedocs.io"
-Repository = "https://github.com/BeckLaboratory/pav"
-Issues = "https://github.com/BeckLaboratory/pav/issues"
-Changelog = "https://github.com/BeckLaboratory/pav/blob/master/CHANGELOG.md"
-
 keywords = [
     "variant calling",
     "variant discovery",
@@ -67,6 +54,16 @@ maintainers = [
     {name = "Peter Audano", email = "peter.audano@jax.org"}
 ]
 
+[project.scripts]
+pav3 = "pav3.cli:main"
+
+[project.urls]
+Homepage = "https://github.com/BeckLaboratory/pav3"
+Documentation = "https://pav3.readthedocs.io"
+Repository = "https://github.com/BeckLaboratory/pav3"
+Issues = "https://github.com/BeckLaboratory/pav3/issues"
+Changelog = "https://github.com/BeckLaboratory/pav3/blob/main/CHANGELOG.md"
+
 [dependency-groups]
 dev = [
     "adbc-driver-manager>=1.7.0",

{pav3-3.0.0.dev23 → pav3-3.0.0.dev26}/src/pav3/__init__.py

@@ -1,6 +1,9 @@
 """PAV Python library routines."""
 
-__version__ = '3.0.0.dev23'
+import importlib
+import logging
+
+__version__ = '3.0.0.dev26'
 
 __all__ = [
     'align',
@@ -8,11 +11,14 @@ __all__ = [
     'call',
     'cli',
     'const',
+    'errors',
     'fig',
+    'format',
     'io',
     'inv',
     'kde',
     'lgsv',
+    'maketable',
     'params',
     'pipeline',
     'region',
@@ -56,7 +62,9 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
 """
 
-import importlib
-
 for name in __all__:
     globals()[name] = importlib.import_module(f'.{name}', package=__name__)
+
+
+# Configure logging
+logging.getLogger(__name__).addHandler(logging.NullHandler())

{pav3-3.0.0.dev23 → pav3-3.0.0.dev26}/src/pav3/align/lift.py

@@ -58,6 +58,7 @@ poor alignment record is not prioritized over one where both coordinates land on
 alignment record.
 
 Values:
+
 * score: Prioritize by the alignment record scores. First by the lowest score, then by the highest.
 * filter: Prioritize by the lesser number of values in the alignment record "filter", first on
   the record with more filters, then on the record with fewer filters.
@@ -69,6 +70,7 @@ Values:
   if a lift switches alignment records.
 
 Keys:
+
 * best: Prioritize on the best alignment records (score, filter, len, single_align, same_align).
 * align: Same align, then best (same_align, score, filter, len, single_align).
 * len: Same region length, then best (len, score, filter, single_align, same_align).
@@ -391,6 +393,7 @@ class AlignLift:
         """Lift coordinates from query to reference.
 
         Each dict has the following keys:
+
         - chrom: Reference chromosome
         - pos: Reference position in 0-based coordinates.
         - is_rev: Whether the query is reverse-complemented in this alignment
@@ -456,6 +459,7 @@ class AlignLift:
         """Lift coordinates from reference to query.
 
         Each dict has the following keys:
+
         - chrom: Query ID
         - pos: Query position in 0-based coordinates
         - is_rev: Whether the query is reverse-complemented