Resolve merge conflicts with branch demulti_fixed

rouskinlab · Nov 8, 2023 · d6ab074 · d6ab074
2 parents 6f0a97e + b54f498
commit d6ab074
Show file tree

Hide file tree

Showing 332 changed files with 29,138 additions and 15,851 deletions.
diff --git a/docs/.doctrees/about/index.doctree b/docs/.doctrees/about/index.doctree
diff --git a/docs/.doctrees/api/seismicrna.align.doctree b/docs/.doctrees/api/seismicrna.align.doctree
diff --git a/docs/.doctrees/api/seismicrna.align.tests.doctree b/docs/.doctrees/api/seismicrna.align.tests.doctree
diff --git a/docs/.doctrees/api/seismicrna.cluster.doctree b/docs/.doctrees/api/seismicrna.cluster.doctree
diff --git a/docs/.doctrees/api/seismicrna.core.arg.doctree b/docs/.doctrees/api/seismicrna.core.arg.doctree
diff --git a/docs/.doctrees/api/seismicrna.core.batch.doctree b/docs/.doctrees/api/seismicrna.core.batch.doctree
diff --git a/docs/.doctrees/api/seismicrna.core.doctree b/docs/.doctrees/api/seismicrna.core.doctree
diff --git a/docs/.doctrees/api/seismicrna.core.extern.doctree b/docs/.doctrees/api/seismicrna.core.extern.doctree
diff --git a/docs/.doctrees/api/seismicrna.core.io.doctree b/docs/.doctrees/api/seismicrna.core.io.doctree
diff --git a/docs/.doctrees/api/seismicrna.core.meta.doctree b/docs/.doctrees/api/seismicrna.core.meta.doctree
diff --git a/docs/.doctrees/api/seismicrna.core.mu.doctree b/docs/.doctrees/api/seismicrna.core.mu.doctree
diff --git a/docs/.doctrees/api/seismicrna.core.mu.tests.doctree b/docs/.doctrees/api/seismicrna.core.mu.tests.doctree
diff --git a/docs/.doctrees/api/seismicrna.core.ngs.doctree b/docs/.doctrees/api/seismicrna.core.ngs.doctree
diff --git a/docs/.doctrees/api/seismicrna.core.ngs.tests.doctree b/docs/.doctrees/api/seismicrna.core.ngs.tests.doctree
diff --git a/docs/.doctrees/api/seismicrna.core.parallel.doctree b/docs/.doctrees/api/seismicrna.core.parallel.doctree
diff --git a/docs/.doctrees/api/seismicrna.core.parallel.tests.doctree b/docs/.doctrees/api/seismicrna.core.parallel.tests.doctree
diff --git a/docs/.doctrees/api/seismicrna.core.rel.doctree b/docs/.doctrees/api/seismicrna.core.rel.doctree
diff --git a/docs/.doctrees/api/seismicrna.core.rel.tests.doctree b/docs/.doctrees/api/seismicrna.core.rel.tests.doctree
diff --git a/docs/.doctrees/api/seismicrna.core.rna.doctree b/docs/.doctrees/api/seismicrna.core.rna.doctree
diff --git a/docs/.doctrees/api/seismicrna.core.seq.doctree b/docs/.doctrees/api/seismicrna.core.seq.doctree
diff --git a/docs/.doctrees/api/seismicrna.core.seq.tests.doctree b/docs/.doctrees/api/seismicrna.core.seq.tests.doctree
diff --git a/docs/.doctrees/api/seismicrna.core.tests.doctree b/docs/.doctrees/api/seismicrna.core.tests.doctree
diff --git a/docs/.doctrees/api/seismicrna.fastc.doctree b/docs/.doctrees/api/seismicrna.fastc.doctree
diff --git a/docs/.doctrees/api/seismicrna.fold.doctree b/docs/.doctrees/api/seismicrna.fold.doctree
diff --git a/docs/.doctrees/api/seismicrna.graph.doctree b/docs/.doctrees/api/seismicrna.graph.doctree
diff --git a/docs/.doctrees/api/seismicrna.mask.doctree b/docs/.doctrees/api/seismicrna.mask.doctree
diff --git a/docs/.doctrees/api/seismicrna.relate.aux.doctree b/docs/.doctrees/api/seismicrna.relate.aux.doctree
diff --git a/docs/.doctrees/api/seismicrna.relate.aux.tests.doctree b/docs/.doctrees/api/seismicrna.relate.aux.tests.doctree
diff --git a/docs/.doctrees/api/seismicrna.relate.c.doctree b/docs/.doctrees/api/seismicrna.relate.c.doctree
diff --git a/docs/.doctrees/api/seismicrna.relate.doctree b/docs/.doctrees/api/seismicrna.relate.doctree
diff --git a/docs/.doctrees/api/seismicrna.relate.py.doctree b/docs/.doctrees/api/seismicrna.relate.py.doctree
diff --git a/docs/.doctrees/api/seismicrna.relate.py.tests.doctree b/docs/.doctrees/api/seismicrna.relate.py.tests.doctree
diff --git a/docs/.doctrees/api/seismicrna.relate.tests.doctree b/docs/.doctrees/api/seismicrna.relate.tests.doctree
diff --git a/docs/.doctrees/api/seismicrna.sim.doctree b/docs/.doctrees/api/seismicrna.sim.doctree
diff --git a/docs/.doctrees/api/seismicrna.sim.tests.doctree b/docs/.doctrees/api/seismicrna.sim.tests.doctree
diff --git a/docs/.doctrees/api/seismicrna.table.doctree b/docs/.doctrees/api/seismicrna.table.doctree
diff --git a/docs/.doctrees/api/seismicrna.whole.doctree b/docs/.doctrees/api/seismicrna.whole.doctree
diff --git a/docs/.doctrees/cli.doctree b/docs/.doctrees/cli.doctree
diff --git a/docs/.doctrees/data/index.doctree b/docs/.doctrees/data/index.doctree
diff --git a/docs/.doctrees/environment.pickle b/docs/.doctrees/environment.pickle
diff --git a/docs/.doctrees/formats/data/index.doctree b/docs/.doctrees/formats/data/index.doctree
diff --git a/docs/.doctrees/install/conda.doctree b/docs/.doctrees/install/conda.doctree
diff --git a/docs/.doctrees/manuals/steps/align.doctree b/docs/.doctrees/manuals/steps/align.doctree
diff --git a/docs/.doctrees/manuals/steps/index.doctree b/docs/.doctrees/manuals/steps/index.doctree
diff --git a/docs/.doctrees/tutorials/example.doctree b/docs/.doctrees/tutorials/example.doctree
diff --git a/docs/_sources/api/seismicrna.align.rst.txt b/docs/_sources/api/seismicrna.align.rst.txt
@@ -18,37 +18,43 @@ Submodules
 ----------
 
 
-.. automodule:: seismicrna.align.fq2bam
+.. automodule:: seismicrna.align.fqops
    :members:
    :undoc-members:
    :show-inheritance:
 
 
-.. automodule:: seismicrna.align.fqops
+.. automodule:: seismicrna.align.fqunit
    :members:
    :undoc-members:
    :show-inheritance:
 
 
-.. automodule:: seismicrna.align.fqunit
+.. automodule:: seismicrna.align.main
    :members:
    :undoc-members:
    :show-inheritance:
 
 
-.. automodule:: seismicrna.align.main
+.. automodule:: seismicrna.align.report
    :members:
    :undoc-members:
    :show-inheritance:
 
 
-.. automodule:: seismicrna.align.report
+.. automodule:: seismicrna.align.sim
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: seismicrna.align.write
    :members:
    :undoc-members:
    :show-inheritance:
 
 
-.. automodule:: seismicrna.align.xamgen
+.. automodule:: seismicrna.align.xamops
    :members:
    :undoc-members:
    :show-inheritance:
diff --git a/docs/_sources/api/seismicrna.align.tests.rst.txt b/docs/_sources/api/seismicrna.align.tests.rst.txt
@@ -16,6 +16,12 @@ Submodules
    :show-inheritance:
 
 
+.. automodule:: seismicrna.align.tests.sim_test
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 .. automodule:: seismicrna.align.tests.xamgen_test
    :members:
    :undoc-members:

diff --git a/docs/_sources/api/seismicrna.cluster.rst.txt b/docs/_sources/api/seismicrna.cluster.rst.txt
@@ -10,25 +10,37 @@ Submodules
 ----------
 
 
+.. automodule:: seismicrna.cluster.batch
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 .. automodule:: seismicrna.cluster.compare
    :members:
    :undoc-members:
    :show-inheritance:
 
 
-.. automodule:: seismicrna.cluster.em
+.. automodule:: seismicrna.cluster.csv
    :members:
    :undoc-members:
    :show-inheritance:
 
 
-.. automodule:: seismicrna.cluster.krun
+.. automodule:: seismicrna.cluster.data
    :members:
    :undoc-members:
    :show-inheritance:
 
 
-.. automodule:: seismicrna.cluster.load
+.. automodule:: seismicrna.cluster.em
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: seismicrna.cluster.io
    :members:
    :undoc-members:
    :show-inheritance:
@@ -52,6 +64,12 @@ Submodules
    :show-inheritance:
 
 
+.. automodule:: seismicrna.cluster.uniq
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 .. automodule:: seismicrna.cluster.write
    :members:
    :undoc-members:

diff --git a/docs/_sources/api/seismicrna.core.arg.rst.txt b/docs/_sources/api/seismicrna.core.arg.rst.txt
@@ -0,0 +1,28 @@
+seismicrna.core.arg package
+===========================
+
+.. automodule:: seismicrna.core.arg
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+
+.. automodule:: seismicrna.core.arg.cli
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: seismicrna.core.arg.cmd
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: seismicrna.core.arg.docdef
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/_sources/api/seismicrna.core.batch.rst.txt b/docs/_sources/api/seismicrna.core.batch.rst.txt
@@ -0,0 +1,40 @@
+seismicrna.core.batch package
+=============================
+
+.. automodule:: seismicrna.core.batch
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+
+.. automodule:: seismicrna.core.batch.accum
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: seismicrna.core.batch.count
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: seismicrna.core.batch.index
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: seismicrna.core.batch.muts
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: seismicrna.core.batch.read
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/_sources/api/seismicrna.core.extern.rst.txt b/docs/_sources/api/seismicrna.core.extern.rst.txt
@@ -0,0 +1,22 @@
+seismicrna.core.extern package
+==============================
+
+.. automodule:: seismicrna.core.extern
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+
+.. automodule:: seismicrna.core.extern.depend
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: seismicrna.core.extern.shell
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/_sources/api/seismicrna.core.io.rst.txt b/docs/_sources/api/seismicrna.core.io.rst.txt
@@ -0,0 +1,46 @@
+seismicrna.core.io package
+==========================
+
+.. automodule:: seismicrna.core.io
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+
+.. automodule:: seismicrna.core.io.batch
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: seismicrna.core.io.data
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: seismicrna.core.io.file
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: seismicrna.core.io.report
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: seismicrna.core.io.seq
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: seismicrna.core.io.util
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/_sources/api/seismicrna.core.meta.rst.txt b/docs/_sources/api/seismicrna.core.meta.rst.txt
@@ -0,0 +1,16 @@
+seismicrna.core.meta package
+============================
+
+.. automodule:: seismicrna.core.meta
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+
+.. automodule:: seismicrna.core.meta.version
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/_sources/api/seismicrna.core.mu.rst.txt b/docs/_sources/api/seismicrna.core.mu.rst.txt
@@ -0,0 +1,36 @@
+seismicrna.core.mu package
+==========================
+
+.. automodule:: seismicrna.core.mu
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   seismicrna.core.mu.tests
+
+Submodules
+----------
+
+
+.. automodule:: seismicrna.core.mu.frame
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: seismicrna.core.mu.norm
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: seismicrna.core.mu.unbias
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/_sources/api/seismicrna.core.mu.tests.rst.txt b/docs/_sources/api/seismicrna.core.mu.tests.rst.txt
@@ -0,0 +1,28 @@
+seismicrna.core.mu.tests package
+================================
+
+.. automodule:: seismicrna.core.mu.tests
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+
+.. automodule:: seismicrna.core.mu.tests.frame_test
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: seismicrna.core.mu.tests.norm_test
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: seismicrna.core.mu.tests.unbias_test
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/_sources/api/seismicrna.core.ngs.rst.txt b/docs/_sources/api/seismicrna.core.ngs.rst.txt
@@ -0,0 +1,30 @@
+seismicrna.core.ngs package
+===========================
+
+.. automodule:: seismicrna.core.ngs
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   seismicrna.core.ngs.tests
+
+Submodules
+----------
+
+
+.. automodule:: seismicrna.core.ngs.phred
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: seismicrna.core.ngs.xam
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/_sources/api/seismicrna.core.ngs.tests.rst.txt b/docs/_sources/api/seismicrna.core.ngs.tests.rst.txt
@@ -0,0 +1,16 @@
+seismicrna.core.ngs.tests package
+=================================
+
+.. automodule:: seismicrna.core.ngs.tests
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+
+.. automodule:: seismicrna.core.ngs.tests.phred_test
+   :members:
+   :undoc-members:
+   :show-inheritance: