speconsense 0.7.2__tar.gz → 0.7.4__tar.gz

{speconsense-0.7.2/speconsense.egg-info → speconsense-0.7.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: speconsense
-Version: 0.7.2
+Version: 0.7.4
 Summary: High-quality clustering and consensus generation for Oxford Nanopore amplicon reads
 Author-email: Josh Walker <joshowalker@yahoo.com>
 License: BSD-3-Clause
@@ -171,6 +171,7 @@ speconsense input.fastq -p herbarium --min-size 10
 ```
 
 **Bundled profiles:**
+- `compressed` — Compress variants into minimal IUPAC consensus sequences (aggressive merging with indels, 20% thresholds, full consensus, 20% selection size ratio)
 - `herbarium` — High-recall for degraded DNA/type specimens
 - `largedata` — Experimental settings for large input files
 - `nostalgia` — Simulate older bioinformatics pipelines
@@ -294,12 +295,14 @@ When using `speconsense-summarize` for post-processing, creates `__Summary__/` d
 |---------------|-------------|------------|-------------|
 | **Original** | Source `cluster_debug/` | `-c1`, `-c2`, `-c3` | Preserves speconsense clustering results |
 | **Summarization** | `__Summary__/`, `FASTQ Files/`, `variants/` | `-1.v1`, `-1.v2`, `-2.v1`, `.raw1` | Post-processing groups and variants |
+| **Full consensus** | `__Summary__/` | `-1.full` | IUPAC consensus from all pre-merge variants in a group |
 
 ### Example Directory Structure
 ```
 __Summary__/
 ├── sample-1.v1-RiC45.fasta                  # Primary variant (group 1, merged)
 ├── sample-1.v2-RiC23.fasta                  # Additional variant (not merged)
+├── sample-1.full-RiC68.fasta                # Full IUPAC consensus for group 1 (all pre-merge variants)
 ├── sample-2.v1-RiC30.fasta                  # Second organism group, primary variant
 ├── summary.fasta                            # All final consensus sequences (excludes .raw)
 ├── summary.txt                              # Statistics
@@ -675,6 +678,18 @@ speconsense-summarize --select-strategy diversity --select-max-variants 2
    - Output up to select_max_variants per group
 3. Final output contains representatives from all groups, ensuring both biological diversity (between groups) and appropriate sampling within each biological entity (within groups)
 
+**Selection Size Ratio Filtering:**
+```bash
+speconsense-summarize --select-min-size-ratio 0.2
+```
+- Filters out post-merge variants whose size is too small relative to the largest variant in their group
+- Ratio calculated as `variant_size / largest_size` — must be ≥ threshold to keep
+- Example: `--select-min-size-ratio 0.2` means a variant must have ≥20% the reads of the largest variant in its group
+- Default is 0 (disabled) — all post-merge variants pass through to selection
+- Applied after merging but before variant selection
+- Useful for suppressing noise variants that survived merging but are too small to be meaningful
+- Set to 0.2 in the `compressed` profile to match the 20% calling threshold theme
+
 This two-stage process ensures that distinct biological sequences are preserved as separate groups, while providing control over variant complexity within each group.
 
 ### Customizing FASTA Header Fields
@@ -810,6 +825,18 @@ For high-throughput workflows (e.g., 100K sequences/year), this prioritization e
 
 ### Additional Summarize Options
 
+**Full Consensus:**
+```bash
+speconsense-summarize --enable-full-consensus
+```
+- Generates a full IUPAC consensus sequence per variant group from all pre-merge variants
+- Output named `{specimen}-{group}.full-RiC{reads}.fasta` in the `__Summary__/` directory
+- Uses majority voting across all variants in the group; **gaps never win** — at each alignment column, the most common non-gap base is chosen, with IUPAC codes for ties among bases
+- Useful when you want a single representative sequence that captures all variation within a group as IUPAC ambiguity codes
+- Included in `summary.fasta` (but excluded from total RiC to avoid double-counting)
+- Enabled by default in the `compressed` profile
+- Use `--disable-full-consensus` to override when set by a profile
+
 **Quality Filtering:**
 ```bash
 speconsense-summarize --min-ric 5
@@ -1044,8 +1071,10 @@ The complete speconsense-summarize workflow operates in this order:
 2. **HAC variant grouping** by sequence identity to separate dissimilar sequences (`--group-identity`); uses single-linkage when overlap merging is enabled
 3. **Group filtering** to limit output groups (`--select-max-groups`)
 4. **Homopolymer-aware MSA-based variant merging** within each group, including **overlap merging** for different-length sequences (`--disable-merging`, `--merge-effort`, `--merge-position-count`, `--merge-indel-length`, `--min-merge-overlap`, `--merge-snp`, `--merge-min-size-ratio`, `--disable-homopolymer-equivalence`)
-5. **Variant selection** within each group (`--select-max-variants`, `--select-strategy`)
-6. **Output generation** with customizable header fields (`--fasta-fields`) and full traceability
+5. **Selection size ratio filtering** to remove tiny post-merge variants (`--select-min-size-ratio`)
+6. **Variant selection** within each group (`--select-max-variants`, `--select-strategy`)
+7. **Full consensus generation** (optional) — IUPAC consensus from all pre-merge variants per group (`--enable-full-consensus`)
+8. **Output generation** with customizable header fields (`--fasta-fields`) and full traceability
 
 **Key architectural features**:
 - HAC grouping occurs BEFORE merging to prevent inappropriate merging of dissimilar sequences (e.g., contaminants with primary targets)
@@ -1098,17 +1127,20 @@ usage: speconsense [-h] [-O OUTPUT_DIR] [--primers PRIMERS]
                    [--min-cluster-ratio MIN_CLUSTER_RATIO]
                    [--max-sample-size MAX_SAMPLE_SIZE]
                    [--outlier-identity OUTLIER_IDENTITY]
-                   [--disable-position-phasing]
+                   [--disable-position-phasing] [--enable-position-phasing]
                    [--min-variant-frequency MIN_VARIANT_FREQUENCY]
                    [--min-variant-count MIN_VARIANT_COUNT]
-                   [--disable-ambiguity-calling]
+                   [--disable-ambiguity-calling] [--enable-ambiguity-calling]
                    [--min-ambiguity-frequency MIN_AMBIGUITY_FREQUENCY]
                    [--min-ambiguity-count MIN_AMBIGUITY_COUNT]
-                   [--disable-cluster-merging]
+                   [--disable-cluster-merging] [--enable-cluster-merging]
                    [--disable-homopolymer-equivalence]
+                   [--enable-homopolymer-equivalence]
                    [--orient-mode {skip,keep-all,filter-failed}]
                    [--presample PRESAMPLE] [--scale-threshold SCALE_THRESHOLD]
-                   [--threads N] [--enable-early-filter] [--collect-discards]
+                   [--threads N] [--enable-early-filter]
+                   [--disable-early-filter] [--collect-discards]
+                   [--no-collect-discards]
                    [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
                    [--version] [-p NAME] [--list-profiles]
                    input_file
@@ -1167,6 +1199,8 @@ Variant Phasing:
                         default). MCL graph clustering already separates most
                         variants; this second pass analyzes MSA positions to
                         phase remaining variants.
+  --enable-position-phasing
+                        Override --disable-position-phasing or profile setting
   --min-variant-frequency MIN_VARIANT_FREQUENCY
                         Minimum alternative allele frequency to call variant
                         (default: 0.10 for 10%)
@@ -1178,6 +1212,9 @@ Ambiguity Calling:
   --disable-ambiguity-calling
                         Disable IUPAC ambiguity code calling for unphased
                         variant positions
+  --enable-ambiguity-calling
+                        Override --disable-ambiguity-calling or profile
+                        setting
   --min-ambiguity-frequency MIN_AMBIGUITY_FREQUENCY
                         Minimum alternative allele frequency for IUPAC
                         ambiguity calling (default: 0.10 for 10%)
@@ -1189,9 +1226,14 @@ Cluster Merging:
   --disable-cluster-merging
                         Disable merging of clusters with identical consensus
                         sequences
+  --enable-cluster-merging
+                        Override --disable-cluster-merging or profile setting
   --disable-homopolymer-equivalence
                         Disable homopolymer equivalence in cluster merging
                         (only merge identical sequences)
+  --enable-homopolymer-equivalence
+                        Override --disable-homopolymer-equivalence or profile
+                        setting
 
 Orientation:
   --orient-mode {skip,keep-all,filter-failed}
@@ -1213,10 +1255,14 @@ Performance:
                         Enable early filtering to skip small clusters before
                         variant phasing (improves performance for large
                         datasets)
+  --disable-early-filter
+                        Override --enable-early-filter or profile setting
 
 Debugging:
   --collect-discards    Write discarded reads (outliers and filtered clusters)
                         to cluster_debug/{sample}-discards.fastq
+  --no-collect-discards
+                        Override --collect-discards or profile setting
   --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
 ```
 
@@ -1227,15 +1273,22 @@ usage: speconsense-summarize [-h] [--source SOURCE]
                              [--summary-dir SUMMARY_DIR]
                              [--fasta-fields FASTA_FIELDS] [--min-ric MIN_RIC]
                              [--min-len MIN_LEN] [--max-len MAX_LEN]
-                             [--group-identity GROUP_IDENTITY] [--merge-snp]
+                             [--group-identity GROUP_IDENTITY]
+                             [--disable-merging] [--enable-merging]
+                             [--merge-snp | --no-merge-snp]
                              [--merge-indel-length MERGE_INDEL_LENGTH]
                              [--merge-position-count MERGE_POSITION_COUNT]
                              [--merge-min-size-ratio MERGE_MIN_SIZE_RATIO]
                              [--min-merge-overlap MIN_MERGE_OVERLAP]
                              [--disable-homopolymer-equivalence]
+                             [--enable-homopolymer-equivalence]
+                             [--merge-effort LEVEL]
                              [--select-max-groups SELECT_MAX_GROUPS]
                              [--select-max-variants SELECT_MAX_VARIANTS]
                              [--select-strategy {size,diversity}]
+                             [--select-min-size-ratio SELECT_MIN_SIZE_RATIO]
+                             [--enable-full-consensus]
+                             [--disable-full-consensus]
                              [--scale-threshold SCALE_THRESHOLD] [--threads N]
                              [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
                              [--version] [-p NAME] [--list-profiles]
@@ -1281,10 +1334,7 @@ Grouping:
 Merging:
   --disable-merging     Disable all variant merging (skip MSA-based merge
                         evaluation entirely)
-  --merge-effort LEVEL  Merging effort level: fast (8), balanced (10),
-                        thorough (12), or numeric 6-14. Higher values allow
-                        larger batch sizes for exhaustive subset search.
-                        Default: balanced
+  --enable-merging      Override --disable-merging or profile setting
   --merge-snp, --no-merge-snp
                         Enable SNP-based merging (default: True, use --no-
                         merge-snp to disable)
@@ -1303,6 +1353,13 @@ Merging:
   --disable-homopolymer-equivalence
                         Disable homopolymer equivalence in merging (treat AAA
                         vs AAAA as different)
+  --enable-homopolymer-equivalence
+                        Override --disable-homopolymer-equivalence or profile
+                        setting
+  --merge-effort LEVEL  Merging effort level: fast (8), balanced (10),
+                        thorough (12), or numeric 6-14. Higher values allow
+                        larger batch sizes for exhaustive subset search.
+                        Default: balanced
 
 Selection:
   --select-max-groups SELECT_MAX_GROUPS, --max-groups SELECT_MAX_GROUPS
@@ -1314,6 +1371,16 @@ Selection:
   --select-strategy {size,diversity}, --variant-selection {size,diversity}
                         Variant selection strategy: size or diversity
                         (default: size)
+  --select-min-size-ratio SELECT_MIN_SIZE_RATIO
+                        Minimum size ratio (variant/largest) to include in
+                        output (default: 0 = disabled, e.g. 0.2 for 20%
+                        cutoff)
+  --enable-full-consensus
+                        Generate a full consensus per variant group
+                        representing all variation from pre-merge variants
+                        (gaps never win)
+  --disable-full-consensus
+                        Override --enable-full-consensus or profile setting
 
 Performance:
   --scale-threshold SCALE_THRESHOLD

{speconsense-0.7.2 → speconsense-0.7.4}/README.md

@@ -136,6 +136,7 @@ speconsense input.fastq -p herbarium --min-size 10
 ```
 
 **Bundled profiles:**
+- `compressed` — Compress variants into minimal IUPAC consensus sequences (aggressive merging with indels, 20% thresholds, full consensus, 20% selection size ratio)
 - `herbarium` — High-recall for degraded DNA/type specimens
 - `largedata` — Experimental settings for large input files
 - `nostalgia` — Simulate older bioinformatics pipelines
@@ -259,12 +260,14 @@ When using `speconsense-summarize` for post-processing, creates `__Summary__/` d
 |---------------|-------------|------------|-------------|
 | **Original** | Source `cluster_debug/` | `-c1`, `-c2`, `-c3` | Preserves speconsense clustering results |
 | **Summarization** | `__Summary__/`, `FASTQ Files/`, `variants/` | `-1.v1`, `-1.v2`, `-2.v1`, `.raw1` | Post-processing groups and variants |
+| **Full consensus** | `__Summary__/` | `-1.full` | IUPAC consensus from all pre-merge variants in a group |
 
 ### Example Directory Structure
 ```
 __Summary__/
 ├── sample-1.v1-RiC45.fasta                  # Primary variant (group 1, merged)
 ├── sample-1.v2-RiC23.fasta                  # Additional variant (not merged)
+├── sample-1.full-RiC68.fasta                # Full IUPAC consensus for group 1 (all pre-merge variants)
 ├── sample-2.v1-RiC30.fasta                  # Second organism group, primary variant
 ├── summary.fasta                            # All final consensus sequences (excludes .raw)
 ├── summary.txt                              # Statistics
@@ -640,6 +643,18 @@ speconsense-summarize --select-strategy diversity --select-max-variants 2
    - Output up to select_max_variants per group
 3. Final output contains representatives from all groups, ensuring both biological diversity (between groups) and appropriate sampling within each biological entity (within groups)
 
+**Selection Size Ratio Filtering:**
+```bash
+speconsense-summarize --select-min-size-ratio 0.2
+```
+- Filters out post-merge variants whose size is too small relative to the largest variant in their group
+- Ratio calculated as `variant_size / largest_size` — must be ≥ threshold to keep
+- Example: `--select-min-size-ratio 0.2` means a variant must have ≥20% the reads of the largest variant in its group
+- Default is 0 (disabled) — all post-merge variants pass through to selection
+- Applied after merging but before variant selection
+- Useful for suppressing noise variants that survived merging but are too small to be meaningful
+- Set to 0.2 in the `compressed` profile to match the 20% calling threshold theme
+
 This two-stage process ensures that distinct biological sequences are preserved as separate groups, while providing control over variant complexity within each group.
 
 ### Customizing FASTA Header Fields
@@ -775,6 +790,18 @@ For high-throughput workflows (e.g., 100K sequences/year), this prioritization e
 
 ### Additional Summarize Options
 
+**Full Consensus:**
+```bash
+speconsense-summarize --enable-full-consensus
+```
+- Generates a full IUPAC consensus sequence per variant group from all pre-merge variants
+- Output named `{specimen}-{group}.full-RiC{reads}.fasta` in the `__Summary__/` directory
+- Uses majority voting across all variants in the group; **gaps never win** — at each alignment column, the most common non-gap base is chosen, with IUPAC codes for ties among bases
+- Useful when you want a single representative sequence that captures all variation within a group as IUPAC ambiguity codes
+- Included in `summary.fasta` (but excluded from total RiC to avoid double-counting)
+- Enabled by default in the `compressed` profile
+- Use `--disable-full-consensus` to override when set by a profile
+
 **Quality Filtering:**
 ```bash
 speconsense-summarize --min-ric 5
@@ -1009,8 +1036,10 @@ The complete speconsense-summarize workflow operates in this order:
 2. **HAC variant grouping** by sequence identity to separate dissimilar sequences (`--group-identity`); uses single-linkage when overlap merging is enabled
 3. **Group filtering** to limit output groups (`--select-max-groups`)
 4. **Homopolymer-aware MSA-based variant merging** within each group, including **overlap merging** for different-length sequences (`--disable-merging`, `--merge-effort`, `--merge-position-count`, `--merge-indel-length`, `--min-merge-overlap`, `--merge-snp`, `--merge-min-size-ratio`, `--disable-homopolymer-equivalence`)
-5. **Variant selection** within each group (`--select-max-variants`, `--select-strategy`)
-6. **Output generation** with customizable header fields (`--fasta-fields`) and full traceability
+5. **Selection size ratio filtering** to remove tiny post-merge variants (`--select-min-size-ratio`)
+6. **Variant selection** within each group (`--select-max-variants`, `--select-strategy`)
+7. **Full consensus generation** (optional) — IUPAC consensus from all pre-merge variants per group (`--enable-full-consensus`)
+8. **Output generation** with customizable header fields (`--fasta-fields`) and full traceability
 
 **Key architectural features**:
 - HAC grouping occurs BEFORE merging to prevent inappropriate merging of dissimilar sequences (e.g., contaminants with primary targets)
@@ -1063,17 +1092,20 @@ usage: speconsense [-h] [-O OUTPUT_DIR] [--primers PRIMERS]
                    [--min-cluster-ratio MIN_CLUSTER_RATIO]
                    [--max-sample-size MAX_SAMPLE_SIZE]
                    [--outlier-identity OUTLIER_IDENTITY]
-                   [--disable-position-phasing]
+                   [--disable-position-phasing] [--enable-position-phasing]
                    [--min-variant-frequency MIN_VARIANT_FREQUENCY]
                    [--min-variant-count MIN_VARIANT_COUNT]
-                   [--disable-ambiguity-calling]
+                   [--disable-ambiguity-calling] [--enable-ambiguity-calling]
                    [--min-ambiguity-frequency MIN_AMBIGUITY_FREQUENCY]
                    [--min-ambiguity-count MIN_AMBIGUITY_COUNT]
-                   [--disable-cluster-merging]
+                   [--disable-cluster-merging] [--enable-cluster-merging]
                    [--disable-homopolymer-equivalence]
+                   [--enable-homopolymer-equivalence]
                    [--orient-mode {skip,keep-all,filter-failed}]
                    [--presample PRESAMPLE] [--scale-threshold SCALE_THRESHOLD]
-                   [--threads N] [--enable-early-filter] [--collect-discards]
+                   [--threads N] [--enable-early-filter]
+                   [--disable-early-filter] [--collect-discards]
+                   [--no-collect-discards]
                    [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
                    [--version] [-p NAME] [--list-profiles]
                    input_file
@@ -1132,6 +1164,8 @@ Variant Phasing:
                         default). MCL graph clustering already separates most
                         variants; this second pass analyzes MSA positions to
                         phase remaining variants.
+  --enable-position-phasing
+                        Override --disable-position-phasing or profile setting
   --min-variant-frequency MIN_VARIANT_FREQUENCY
                         Minimum alternative allele frequency to call variant
                         (default: 0.10 for 10%)
@@ -1143,6 +1177,9 @@ Ambiguity Calling:
   --disable-ambiguity-calling
                         Disable IUPAC ambiguity code calling for unphased
                         variant positions
+  --enable-ambiguity-calling
+                        Override --disable-ambiguity-calling or profile
+                        setting
   --min-ambiguity-frequency MIN_AMBIGUITY_FREQUENCY
                         Minimum alternative allele frequency for IUPAC
                         ambiguity calling (default: 0.10 for 10%)
@@ -1154,9 +1191,14 @@ Cluster Merging:
   --disable-cluster-merging
                         Disable merging of clusters with identical consensus
                         sequences
+  --enable-cluster-merging
+                        Override --disable-cluster-merging or profile setting
   --disable-homopolymer-equivalence
                         Disable homopolymer equivalence in cluster merging
                         (only merge identical sequences)
+  --enable-homopolymer-equivalence
+                        Override --disable-homopolymer-equivalence or profile
+                        setting
 
 Orientation:
   --orient-mode {skip,keep-all,filter-failed}
@@ -1178,10 +1220,14 @@ Performance:
                         Enable early filtering to skip small clusters before
                         variant phasing (improves performance for large
                         datasets)
+  --disable-early-filter
+                        Override --enable-early-filter or profile setting
 
 Debugging:
   --collect-discards    Write discarded reads (outliers and filtered clusters)
                         to cluster_debug/{sample}-discards.fastq
+  --no-collect-discards
+                        Override --collect-discards or profile setting
   --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
 ```
 
@@ -1192,15 +1238,22 @@ usage: speconsense-summarize [-h] [--source SOURCE]
                              [--summary-dir SUMMARY_DIR]
                              [--fasta-fields FASTA_FIELDS] [--min-ric MIN_RIC]
                              [--min-len MIN_LEN] [--max-len MAX_LEN]
-                             [--group-identity GROUP_IDENTITY] [--merge-snp]
+                             [--group-identity GROUP_IDENTITY]
+                             [--disable-merging] [--enable-merging]
+                             [--merge-snp | --no-merge-snp]
                              [--merge-indel-length MERGE_INDEL_LENGTH]
                              [--merge-position-count MERGE_POSITION_COUNT]
                              [--merge-min-size-ratio MERGE_MIN_SIZE_RATIO]
                              [--min-merge-overlap MIN_MERGE_OVERLAP]
                              [--disable-homopolymer-equivalence]
+                             [--enable-homopolymer-equivalence]
+                             [--merge-effort LEVEL]
                              [--select-max-groups SELECT_MAX_GROUPS]
                              [--select-max-variants SELECT_MAX_VARIANTS]
                              [--select-strategy {size,diversity}]
+                             [--select-min-size-ratio SELECT_MIN_SIZE_RATIO]
+                             [--enable-full-consensus]
+                             [--disable-full-consensus]
                              [--scale-threshold SCALE_THRESHOLD] [--threads N]
                              [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
                              [--version] [-p NAME] [--list-profiles]
@@ -1246,10 +1299,7 @@ Grouping:
 Merging:
   --disable-merging     Disable all variant merging (skip MSA-based merge
                         evaluation entirely)
-  --merge-effort LEVEL  Merging effort level: fast (8), balanced (10),
-                        thorough (12), or numeric 6-14. Higher values allow
-                        larger batch sizes for exhaustive subset search.
-                        Default: balanced
+  --enable-merging      Override --disable-merging or profile setting
   --merge-snp, --no-merge-snp
                         Enable SNP-based merging (default: True, use --no-
                         merge-snp to disable)
@@ -1268,6 +1318,13 @@ Merging:
   --disable-homopolymer-equivalence
                         Disable homopolymer equivalence in merging (treat AAA
                         vs AAAA as different)
+  --enable-homopolymer-equivalence
+                        Override --disable-homopolymer-equivalence or profile
+                        setting
+  --merge-effort LEVEL  Merging effort level: fast (8), balanced (10),
+                        thorough (12), or numeric 6-14. Higher values allow
+                        larger batch sizes for exhaustive subset search.
+                        Default: balanced
 
 Selection:
   --select-max-groups SELECT_MAX_GROUPS, --max-groups SELECT_MAX_GROUPS
@@ -1279,6 +1336,16 @@ Selection:
   --select-strategy {size,diversity}, --variant-selection {size,diversity}
                         Variant selection strategy: size or diversity
                         (default: size)
+  --select-min-size-ratio SELECT_MIN_SIZE_RATIO
+                        Minimum size ratio (variant/largest) to include in
+                        output (default: 0 = disabled, e.g. 0.2 for 20%
+                        cutoff)
+  --enable-full-consensus
+                        Generate a full consensus per variant group
+                        representing all variation from pre-merge variants
+                        (gaps never win)
+  --disable-full-consensus
+                        Override --enable-full-consensus or profile setting
 
 Performance:
   --scale-threshold SCALE_THRESHOLD

{speconsense-0.7.2 → speconsense-0.7.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "speconsense"
-version = "0.7.2"
+version = "0.7.4"
 description = "High-quality clustering and consensus generation for Oxford Nanopore amplicon reads"
 readme = "README.md"
 requires-python = ">=3.8"

{speconsense-0.7.2 → speconsense-0.7.4}/speconsense/__init__.py

@@ -5,7 +5,7 @@ A Python tool for experimental clustering and consensus generation as an alterna
 in the fungal DNA barcoding pipeline.
 """
 
-__version__ = "0.7.2"
+__version__ = "0.7.4"
 __author__ = "Josh Walker"
 __email__ = "joshowalker@yahoo.com"
 

{speconsense-0.7.2 → speconsense-0.7.4}/speconsense/core/cli.py

@@ -66,6 +66,9 @@ def main():
                                help="Disable position-based variant phasing (enabled by default). "
                                     "MCL graph clustering already separates most variants; this "
                                     "second pass analyzes MSA positions to phase remaining variants.")
+    phasing_group.add_argument("--enable-position-phasing", action="store_false",
+                               dest="disable_position_phasing",
+                               help="Override --disable-position-phasing or profile setting")
     phasing_group.add_argument("--min-variant-frequency", type=float, default=0.10,
                                help="Minimum alternative allele frequency to call variant (default: 0.10 for 10%%)")
     phasing_group.add_argument("--min-variant-count", type=int, default=5,
@@ -75,6 +78,9 @@ def main():
     ambiguity_group = parser.add_argument_group("Ambiguity Calling")
     ambiguity_group.add_argument("--disable-ambiguity-calling", action="store_true",
                                  help="Disable IUPAC ambiguity code calling for unphased variant positions")
+    ambiguity_group.add_argument("--enable-ambiguity-calling", action="store_false",
+                                 dest="disable_ambiguity_calling",
+                                 help="Override --disable-ambiguity-calling or profile setting")
     ambiguity_group.add_argument("--min-ambiguity-frequency", type=float, default=0.10,
                                  help="Minimum alternative allele frequency for IUPAC ambiguity calling (default: 0.10 for 10%%)")
     ambiguity_group.add_argument("--min-ambiguity-count", type=int, default=3,
@@ -84,8 +90,14 @@ def main():
     merging_group = parser.add_argument_group("Cluster Merging")
     merging_group.add_argument("--disable-cluster-merging", action="store_true",
                                help="Disable merging of clusters with identical consensus sequences")
+    merging_group.add_argument("--enable-cluster-merging", action="store_false",
+                               dest="disable_cluster_merging",
+                               help="Override --disable-cluster-merging or profile setting")
     merging_group.add_argument("--disable-homopolymer-equivalence", action="store_true",
                                help="Disable homopolymer equivalence in cluster merging (only merge identical sequences)")
+    merging_group.add_argument("--enable-homopolymer-equivalence", action="store_false",
+                               dest="disable_homopolymer_equivalence",
+                               help="Override --disable-homopolymer-equivalence or profile setting")
 
     # Orientation group
     orient_group = parser.add_argument_group("Orientation")
@@ -104,11 +116,17 @@ def main():
                                  "0=auto-detect, default=1 (safe for parallel workflows).")
     perf_group.add_argument("--enable-early-filter", action="store_true",
                             help="Enable early filtering to skip small clusters before variant phasing (improves performance for large datasets)")
+    perf_group.add_argument("--disable-early-filter", action="store_false",
+                            dest="enable_early_filter",
+                            help="Override --enable-early-filter or profile setting")
 
     # Debugging group
     debug_group = parser.add_argument_group("Debugging")
     debug_group.add_argument("--collect-discards", action="store_true",
                              help="Write discarded reads (outliers and filtered clusters) to cluster_debug/{sample}-discards.fastq")
+    debug_group.add_argument("--no-collect-discards", action="store_false",
+                             dest="collect_discards",
+                             help="Override --collect-discards or profile setting")
     debug_group.add_argument("--log-level", default="INFO",
                              choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"])
 

{speconsense-0.7.2 → speconsense-0.7.4}/speconsense/profiles/__init__.py

@@ -103,6 +103,8 @@ VALID_SUMMARIZE_KEYS = {
     "select-max-groups",
     "select-max-variants",
     "select-strategy",
+    "select-min-size-ratio",
+    "enable-full-consensus",
     # Processing
     "scale-threshold",
     "threads",

speconsense-0.7.4/speconsense/profiles/compressed.yaml

@@ -0,0 +1,28 @@
+# Compress variants into minimal IUPAC consensus sequences
+#
+# Aggressively merges similar variants (including indels) into single
+# IUPAC consensus sequences. Only truly dissimilar sequences remain
+# separate. Uses 20% frequency thresholds throughout.
+#
+# Designed for workflows where reviewers want fewer sequences to
+# examine, with all variation represented via IUPAC ambiguity codes.
+# Partial overlap merging is disabled as a safety measure.
+#
+# Use with:
+#   speconsense input.fastq -p compressed
+#   speconsense-summarize -p compressed
+
+speconsense-version: "0.7.*"
+description: "Compress variants into minimal IUPAC consensus sequences"
+
+speconsense:
+  min-ambiguity-frequency: 0.20  # 20% threshold for IUPAC ambiguity calling
+  min-variant-frequency: 0.20   # 20% threshold for variant phasing
+
+speconsense-summarize:
+  merge-indel-length: 5         # Merge indels up to 5bp
+  merge-position-count: 10      # Allow up to 10 variant positions in a merge
+  merge-min-size-ratio: 0.2     # Match 20% calling threshold
+  select-min-size-ratio: 0.2    # Match 20% calling threshold
+  min-merge-overlap: 0          # Disable partial overlap merging
+  enable-full-consensus: true   # Include full IUPAC consensus per group

{speconsense-0.7.2 → speconsense-0.7.4}/speconsense/profiles/example.yaml

@@ -91,6 +91,7 @@ speconsense-summarize:
   # select-max-groups: -1         # Max groups to output (-1 = no limit)
   # select-max-variants: -1       # Max variants per group (-1 = no limit)
   # select-strategy: size         # Selection strategy: size or diversity
+  # select-min-size-ratio: 0    # Min size ratio to include variant (0 = disabled)
 
   # --- Processing ---
   # threads: 0                    # Max threads (0 = auto-detect)