Fasten normalize (#14)

* extra read entry columns in fasten_kmer * single end normalizing * paired end kmer counting with remembering reads * docs for normalizing * mkdir reportsDir * rm -rf docs-md * additional inline docs * add in unit tests for this branch
lskatz · Jan 5, 2023 · 1ed052d · 1ed052d
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diff --git a/.github/workflows/basic.yml b/.github/workflows/basic.yml
@@ -1,6 +1,6 @@
 on: 
   push:
-    branches: [master,main,unit-test]
+    branches: [master,main,unit-test,fasten_normalize]
 
 
 name: CI

diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml
@@ -1,6 +1,6 @@
 on: 
   push:
-    branches: [master,benchmarking]
+    branches: [master,benchmarking,fasten_normalize]
 
 
 name: benchmarking

diff --git a/Cargo.toml b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name    = "fasten"
-version = "0.4.4"
+version = "0.5.0"
 authors = ["Lee Katz <[email protected]>"]
 #license-file  = "LICENSE"
 license       = "MIT"
@@ -83,6 +83,10 @@ path = "src/bin/fasten_progress.rs"
 name = "fasten_sort"
 path = "src/bin/fasten_sort.rs"
 
+[[bin]]
+name = "fasten_normalize"
+path = "src/bin/fasten_normalize.rs"
+
 [dependencies]
 regex        = "0.2.10"
 getopts      = "0.2.21"

diff --git a/docs-md/bin/fasten_clean.md b/docs-md/bin/fasten_clean.md
diff --git a/docs-md/bin/fasten_combine.md b/docs-md/bin/fasten_combine.md
diff --git a/docs-md/bin/fasten_convert.md b/docs-md/bin/fasten_convert.md
diff --git a/docs-md/bin/fasten_kmer.md b/docs-md/bin/fasten_kmer.md
diff --git a/docs-md/bin/fasten_metrics.md b/docs-md/bin/fasten_metrics.md
diff --git a/docs-md/bin/fasten_mutate.md b/docs-md/bin/fasten_mutate.md
diff --git a/docs-md/bin/fasten_pe.md b/docs-md/bin/fasten_pe.md
diff --git a/docs-md/bin/fasten_progress.md b/docs-md/bin/fasten_progress.md
diff --git a/docs-md/bin/fasten_quality_filter.md b/docs-md/bin/fasten_quality_filter.md
diff --git a/docs-md/bin/fasten_randomize.md b/docs-md/bin/fasten_randomize.md
diff --git a/docs-md/bin/fasten_regex.md b/docs-md/bin/fasten_regex.md
diff --git a/docs-md/bin/fasten_replace.md b/docs-md/bin/fasten_replace.md
diff --git a/docs-md/bin/fasten_sample.md b/docs-md/bin/fasten_sample.md