⬆️ version bump to v4.5

- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5"
- Update version.txt from 4.29 → .30
(automated by Makefile)

autodoc/examples/obiconvert/output.json

@@ -0,0 +1,23 @@
+[
+  {
+    "annotations": {
+      "definition": "Test DNA sequence for FASTA conversion"
+    },
+    "id": "seq001",
+    "sequence": "atcgatcgatcgatcgatcgatcgatcgatcgatcgatcg"
+  },
+  {
+    "annotations": {
+      "definition": "Another test sequence with different nucleotide content"
+    },
+    "id": "seq002",
+    "sequence": "gctagctagctagctagctagctagctagctagctagct"
+  },
+  {
+    "annotations": {
+      "definition": "Third sequence for testing output format"
+    },
+    "id": "seq003",
+    "sequence": "ttaaccggttaaccggttaaccggttaaccggttaaccg"
+  }
+]

autodoc/examples/obicount/out_default.txt

@@ -0,0 +1,7 @@
+time="2026-04-02T19:33:11+02:00" level=info msg="Number of workers set 16"
+time="2026-04-02T19:33:11+02:00" level=info msg="Found 1 files to process"
+time="2026-04-02T19:33:11+02:00" level=info msg="input.fasta mime type: text/fasta"
+entities,n
+variants,5
+reads,5
+symbols,435

autodoc/examples/obicount/out_fastq_reads.txt

@@ -0,0 +1,4 @@
+time="2026-04-02T19:33:38+02:00" level=info msg="Number of workers set 16"
+time="2026-04-02T19:33:38+02:00" level=info msg="Found 1 files to process"
+entities,n
+reads,4

autodoc/examples/obicount/out_symbols.txt

@@ -0,0 +1,5 @@
+time="2026-04-02T19:33:29+02:00" level=info msg="Number of workers set 16"
+time="2026-04-02T19:33:29+02:00" level=info msg="Found 1 files to process"
+time="2026-04-02T19:33:29+02:00" level=info msg="input.fasta mime type: text/fasta"
+entities,n
+symbols,435

autodoc/examples/obicount/out_variants.txt

@@ -0,0 +1,5 @@
+time="2026-04-02T19:33:20+02:00" level=info msg="Number of workers set 16"
+time="2026-04-02T19:33:20+02:00" level=info msg="Found 1 files to process"
+time="2026-04-02T19:33:20+02:00" level=info msg="input.fasta mime type: text/fasta"
+entities,n
+variants,5

autodoc/examples/obiscript/annotate.lua

@@ -0,0 +1,9 @@
+-- Adds a 'sample' attribute by extracting the prefix before the first underscore
+function worker(sequence)
+    local id = sequence:id()
+    local sample = string.match(id, "^(.-)_")
+    if sample then
+        sequence:attribute("sample", sample)
+    end
+    return sequence
+end

autodoc/examples/obiscript/enrich.lua

@@ -0,0 +1,5 @@
+-- Marks each sequence as processed by adding a 'processed' attribute
+function worker(sequence)
+    sequence:attribute("processed", "true")
+    return sequence
+end

autodoc/examples/obiscript/enriched.json

@@ -0,0 +1,38 @@
+[
+  {
+    "annotations": {
+      "definition": "long sequence passes min-length 100 filter",
+      "processed": "true"
+    },
+    "id": "seq001",
+    "qualities": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII",
+    "sequence": "atcgatcgatcgatcgatcgatcgatcgatcgatcgatcgatcgatcgatcgatcgatcgatcgatcgatcgatcgatcgatcgatcgatcgatcgatcgatcgatcgatcgatcgatcg"
+  },
+  {
+    "annotations": {
+      "definition": "short sequence fails min-length 100 filter",
+      "processed": "true"
+    },
+    "id": "seq002",
+    "qualities": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII",
+    "sequence": "gctagctagctagctagctagctagctagctagctagctagctagctagctagctagctagctagctagctagctagcta"
+  },
+  {
+    "annotations": {
+      "definition": "long sequence passes min-length 100 filter",
+      "processed": "true"
+    },
+    "id": "seq003",
+    "qualities": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII",
+    "sequence": "ttaattaattaattaattaattaattaattaattaattaattaattaattaattaattaattaattaattaattaattaattaattaattaattaattaattaattaattaa"
+  },
+  {
+    "annotations": {
+      "definition": "short sequence fails min-length 100 filter",
+      "processed": "true"
+    },
+    "id": "seq004",
+    "qualities": "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII",
+    "sequence": "ccggccggccggccggccggccggccggccggccggccggccggccggccgg"
+  }
+]

autodoc/examples/obiscript/my_script.lua

@@ -0,0 +1,17 @@
+function begin()
+    obicontext.item("compteur", 0)
+end
+
+function worker(sequence)
+    samples = sequence:attribute("merged_sample")
+    samples["tutu"] = 4
+    sequence:attribute("merged_sample", samples)
+    sequence:attribute("toto", 44444)
+    nb = obicontext.inc("compteur")
+    sequence:id("seq_" .. nb)
+    return sequence
+end
+
+function finish()
+    print("compteur = " .. obicontext.item("compteur"))
+end

autodoc/examples/obiscript/process_pairs.lua

@@ -0,0 +1,4 @@
+-- Simple pass-through script: returns each sequence unchanged
+function worker(sequence)
+    return sequence
+end

autodoc/examples/obisummary/out_json.json

@@ -0,0 +1,17 @@
+{
+  "annotations": {
+    "keys": {
+      "scalar": {
+        "count": 5
+      }
+    },
+    "map_attributes": 0,
+    "scalar_attributes": 1,
+    "vector_attributes": 0
+  },
+  "count": {
+    "reads": 21,
+    "total_length": 100,
+    "variants": 5
+  }
+}