From 7b220d3390d157c2381a34e44c82ddd169f357b4 Mon Sep 17 00:00:00 2001
From: gerikson <galina.erikson@gmail.com>
Date: Wed, 22 Jan 2025 11:53:03 +0100
Subject: [PATCH 1/7] Added pytests for bamCoverage and bamCompare

---
 .../deeptools/test/test_r_bamCompare.py       | 88 +++++++++++++++++++
 .../deeptools/test/test_r_bamCoverage.py      | 88 +++++++++++++++++++
 2 files changed, 176 insertions(+)
 create mode 100644 pydeeptools/deeptools/test/test_r_bamCompare.py
 create mode 100644 pydeeptools/deeptools/test/test_r_bamCoverage.py

diff --git a/pydeeptools/deeptools/test/test_r_bamCompare.py b/pydeeptools/deeptools/test/test_r_bamCompare.py
new file mode 100644
index 0000000000..8749669614
--- /dev/null
+++ b/pydeeptools/deeptools/test/test_r_bamCompare.py
@@ -0,0 +1,88 @@
+import pytest
+from deeptools.bamCompare2 import r_bamcompare
+import os.path
+import filecmp
+from os import unlink
+
+ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
+BAMFILE_A = ROOT + "test1.bam"
+BAMFILE_B = ROOT + "test2.bam"
+
+
+def test_r_bamcompare():
+    bamifile1 = BAMFILE_A
+    bamifile2 = BAMFILE_B
+    ofile = ROOT + "r_bamcompare_output.bedgraph"
+    ofiletype  = "bedgraph"
+    norm  = "None"
+    effective_genome_size = 0
+    scalefactorsmethod = "None"
+    operation = "ratio"
+    pseudocount = 0
+    # filtering options
+    ignoreduplicates = False
+    minmappingquality = 0
+    samflaginclude = 0
+    samflagexclude = 0
+    minfraglen = 0
+    maxfraglen = 0
+    nproc = 1
+    _ignorechr = []
+    binsize = 500
+    regions = []
+    verbose = False
+
+    # Call the Rust function
+    r_bamcompare(
+        bamifile1, bamifile2, ofile, ofiletype, norm, effective_genome_size, scalefactorsmethod, operation, 
+        pseudocount, ignoreduplicates, minmappingquality, samflaginclude, samflagexclude, minfraglen, maxfraglen, nproc, 
+        _ignorechr, binsize, regions, verbose
+    )
+    # Add assertions to verify the expected behavior
+    expected = ['3R\t0\t500\t0.6213592\n',
+            '3R\t500\t1000\t0.8252427\n',
+            '3R\t1000\t1500\t0.2\n',]
+    _foo = open(ofile, 'r')
+    resp = _foo.readlines()
+    _foo.close()
+    assert f"{resp}" == f"{expected}", f"{resp} != {expected}"
+    unlink(ofile)
+
+def test_r_bamcompare_RPKM():
+    bamifile1 = BAMFILE_A
+    bamifile2 = BAMFILE_B
+    ofile = ROOT + "r_bamcompare_output.bedgraph"
+    ofiletype  = "bedgraph"
+    norm  = "RPKM"
+    effective_genome_size = 0
+    scalefactorsmethod = "None"
+    operation = "ratio"
+    pseudocount = 0
+    # filtering options
+    ignoreduplicates = False
+    minmappingquality = 0
+    samflaginclude = 0
+    samflagexclude = 0
+    minfraglen = 0
+    maxfraglen = 0
+    nproc = 1
+    _ignorechr = []
+    binsize = 500
+    regions = []
+    verbose = False
+
+    # Call the Rust function
+    r_bamcompare(
+        bamifile1, bamifile2, ofile, ofiletype, norm, effective_genome_size, scalefactorsmethod, operation, 
+        pseudocount, ignoreduplicates, minmappingquality, samflaginclude, samflagexclude, minfraglen, maxfraglen, nproc, 
+        _ignorechr, binsize, regions, verbose
+    )
+    # Add assertions to verify the expected behavior
+    expected = ['3R\t0\t500\t0.6213592\n',
+            '3R\t500\t1000\t0.8252427\n',
+            '3R\t1000\t1500\t0.2\n',]
+    _foo = open(ofile, 'r')
+    resp = _foo.readlines()
+    _foo.close()
+    assert f"{resp}" == f"{expected}", f"{resp} != {expected}"
+    unlink(ofile)
\ No newline at end of file
diff --git a/pydeeptools/deeptools/test/test_r_bamCoverage.py b/pydeeptools/deeptools/test/test_r_bamCoverage.py
new file mode 100644
index 0000000000..8749669614
--- /dev/null
+++ b/pydeeptools/deeptools/test/test_r_bamCoverage.py
@@ -0,0 +1,88 @@
+import pytest
+from deeptools.bamCompare2 import r_bamcompare
+import os.path
+import filecmp
+from os import unlink
+
+ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
+BAMFILE_A = ROOT + "test1.bam"
+BAMFILE_B = ROOT + "test2.bam"
+
+
+def test_r_bamcompare():
+    bamifile1 = BAMFILE_A
+    bamifile2 = BAMFILE_B
+    ofile = ROOT + "r_bamcompare_output.bedgraph"
+    ofiletype  = "bedgraph"
+    norm  = "None"
+    effective_genome_size = 0
+    scalefactorsmethod = "None"
+    operation = "ratio"
+    pseudocount = 0
+    # filtering options
+    ignoreduplicates = False
+    minmappingquality = 0
+    samflaginclude = 0
+    samflagexclude = 0
+    minfraglen = 0
+    maxfraglen = 0
+    nproc = 1
+    _ignorechr = []
+    binsize = 500
+    regions = []
+    verbose = False
+
+    # Call the Rust function
+    r_bamcompare(
+        bamifile1, bamifile2, ofile, ofiletype, norm, effective_genome_size, scalefactorsmethod, operation, 
+        pseudocount, ignoreduplicates, minmappingquality, samflaginclude, samflagexclude, minfraglen, maxfraglen, nproc, 
+        _ignorechr, binsize, regions, verbose
+    )
+    # Add assertions to verify the expected behavior
+    expected = ['3R\t0\t500\t0.6213592\n',
+            '3R\t500\t1000\t0.8252427\n',
+            '3R\t1000\t1500\t0.2\n',]
+    _foo = open(ofile, 'r')
+    resp = _foo.readlines()
+    _foo.close()
+    assert f"{resp}" == f"{expected}", f"{resp} != {expected}"
+    unlink(ofile)
+
+def test_r_bamcompare_RPKM():
+    bamifile1 = BAMFILE_A
+    bamifile2 = BAMFILE_B
+    ofile = ROOT + "r_bamcompare_output.bedgraph"
+    ofiletype  = "bedgraph"
+    norm  = "RPKM"
+    effective_genome_size = 0
+    scalefactorsmethod = "None"
+    operation = "ratio"
+    pseudocount = 0
+    # filtering options
+    ignoreduplicates = False
+    minmappingquality = 0
+    samflaginclude = 0
+    samflagexclude = 0
+    minfraglen = 0
+    maxfraglen = 0
+    nproc = 1
+    _ignorechr = []
+    binsize = 500
+    regions = []
+    verbose = False
+
+    # Call the Rust function
+    r_bamcompare(
+        bamifile1, bamifile2, ofile, ofiletype, norm, effective_genome_size, scalefactorsmethod, operation, 
+        pseudocount, ignoreduplicates, minmappingquality, samflaginclude, samflagexclude, minfraglen, maxfraglen, nproc, 
+        _ignorechr, binsize, regions, verbose
+    )
+    # Add assertions to verify the expected behavior
+    expected = ['3R\t0\t500\t0.6213592\n',
+            '3R\t500\t1000\t0.8252427\n',
+            '3R\t1000\t1500\t0.2\n',]
+    _foo = open(ofile, 'r')
+    resp = _foo.readlines()
+    _foo.close()
+    assert f"{resp}" == f"{expected}", f"{resp} != {expected}"
+    unlink(ofile)
\ No newline at end of file

From f0ab442436ddd503dd63c938d1711025b05ef700 Mon Sep 17 00:00:00 2001
From: gerikson <galina.erikson@gmail.com>
Date: Wed, 22 Jan 2025 15:11:28 +0100
Subject: [PATCH 2/7] Some tests for r_computeMatrix

---
 .../test/test_data/filtered_out_reads.bam     |   0
 .../deeptools/test/test_data/log2ratio.bed    |   3 +
 .../deeptools/test/test_data/test2.bam        | Bin 33925 -> 3157 bytes
 .../deeptools/test/test_data/test2.bam.bai    | Bin 96 -> 96 bytes
 .../deeptools/test/test_data/test4.bam        | Bin 0 -> 25326 bytes
 .../deeptools/test/test_data/test4.bam.bai    | Bin 0 -> 96 bytes
 .../deeptools/test/test_data/test5.bam        | Bin 0 -> 3157 bytes
 .../deeptools/test/test_data/test5.bam.bai    | Bin 0 -> 96 bytes
 .../deeptools/test/test_data/testB.bam.bai    | Bin 96 -> 96 bytes
 .../deeptools/test/test_data/testC.bam        | Bin 0 -> 838 bytes
 .../deeptools/test/test_data/testC.bam.bai    | Bin 0 -> 96 bytes
 .../deeptools/test/test_data/test_paired2.bam | Bin 2257 -> 1412 bytes
 .../deeptools/test/test_r_computeMatrix.py    | 109 ++++++++++++++++++
 13 files changed, 112 insertions(+)
 create mode 100644 pydeeptools/deeptools/test/test_data/filtered_out_reads.bam
 create mode 100644 pydeeptools/deeptools/test/test_data/log2ratio.bed
 create mode 100644 pydeeptools/deeptools/test/test_data/test4.bam
 create mode 100644 pydeeptools/deeptools/test/test_data/test4.bam.bai
 create mode 100644 pydeeptools/deeptools/test/test_data/test5.bam
 create mode 100644 pydeeptools/deeptools/test/test_data/test5.bam.bai
 create mode 100644 pydeeptools/deeptools/test/test_data/testC.bam
 create mode 100644 pydeeptools/deeptools/test/test_data/testC.bam.bai
 create mode 100644 pydeeptools/deeptools/test/test_r_computeMatrix.py

diff --git a/pydeeptools/deeptools/test/test_data/filtered_out_reads.bam b/pydeeptools/deeptools/test/test_data/filtered_out_reads.bam
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/pydeeptools/deeptools/test/test_data/log2ratio.bed b/pydeeptools/deeptools/test/test_data/log2ratio.bed
new file mode 100644
index 0000000000..45e37e23af
--- /dev/null
+++ b/pydeeptools/deeptools/test/test_data/log2ratio.bed
@@ -0,0 +1,3 @@
+3R	0	500	2.1154773
+3R	500	1000	1.4720684
+3R	1000	1500	0
diff --git a/pydeeptools/deeptools/test/test_data/test2.bam b/pydeeptools/deeptools/test/test_data/test2.bam
index c53dc3b90c2d2a2bcf180414d8b4b8fc45be8546..036aa29a5e20736c6e1a188f4a021ed1fda0a2f8 100644
GIT binary patch
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diff --git a/pydeeptools/deeptools/test/test_data/test2.bam.bai b/pydeeptools/deeptools/test/test_data/test2.bam.bai
index 6c98b7fd1a3993b859f994df9f62dd62b6b34f15..1bf8fc654137dff44b6d339bbc11532025ffec46 100644
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diff --git a/pydeeptools/deeptools/test/test_data/test4.bam b/pydeeptools/deeptools/test/test_data/test4.bam
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diff --git a/pydeeptools/deeptools/test/test_data/test4.bam.bai b/pydeeptools/deeptools/test/test_data/test4.bam.bai
new file mode 100644
index 0000000000000000000000000000000000000000..64fcc055612f5d4e8f84cb5627c3d5dec55bb813
GIT binary patch
literal 96
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literal 0
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diff --git a/pydeeptools/deeptools/test/test_data/test5.bam b/pydeeptools/deeptools/test/test_data/test5.bam
new file mode 100644
index 0000000000000000000000000000000000000000..036aa29a5e20736c6e1a188f4a021ed1fda0a2f8
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diff --git a/pydeeptools/deeptools/test/test_data/test5.bam.bai b/pydeeptools/deeptools/test/test_data/test5.bam.bai
new file mode 100644
index 0000000000000000000000000000000000000000..1bf8fc654137dff44b6d339bbc11532025ffec46
GIT binary patch
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literal 0
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diff --git a/pydeeptools/deeptools/test/test_data/testB.bam.bai b/pydeeptools/deeptools/test/test_data/testB.bam.bai
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delta 14
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delta 14
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diff --git a/pydeeptools/deeptools/test/test_data/testC.bam b/pydeeptools/deeptools/test/test_data/testC.bam
new file mode 100644
index 0000000000000000000000000000000000000000..f1ac616b78a326e440766be98e7810b17976a2f2
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literal 0
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diff --git a/pydeeptools/deeptools/test/test_data/testC.bam.bai b/pydeeptools/deeptools/test/test_data/testC.bam.bai
new file mode 100644
index 0000000000000000000000000000000000000000..4d683328b6d54b0622fef1b2df763283701a03b1
GIT binary patch
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literal 0
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diff --git a/pydeeptools/deeptools/test/test_data/test_paired2.bam b/pydeeptools/deeptools/test/test_data/test_paired2.bam
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diff --git a/pydeeptools/deeptools/test/test_r_computeMatrix.py b/pydeeptools/deeptools/test/test_r_computeMatrix.py
new file mode 100644
index 0000000000..a1dddb64f0
--- /dev/null
+++ b/pydeeptools/deeptools/test/test_r_computeMatrix.py
@@ -0,0 +1,109 @@
+import pytest
+from deeptools.computeMatrix2 import r_computematrix  # Adjust the import to your actual module
+import os.path
+import gzip
+import hashlib
+
+root = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
+matrix = root + "computeMatrixOperations.mat.gz"
+bed = root + "computeMatrixOperations.bed"
+rbindMatrix1 = root + "somegenes.txt.gz"
+rbindMatrix2 = root + "othergenes.txt.gz"
+bigwig = root + "testA.bw"
+outnpz = root + "output.mat.npz.gz"
+
+def test_r_computematrix_referencePoint():
+    mode = "reference-point"
+    regionlis = [bed]
+    bwlis = [bigwig]
+    sampleslabel = ["sample1"]
+    upstream = 1000
+    downstream = 1000
+    unscaled5prime = 0
+    unscaled3prime = 0
+    regionbodylength = 0
+    binsize = 50
+    missingdatazero = False
+    metagene = False
+    txnid = ""
+    exonid = ""
+    txniddesignator = ""
+    scale = 1.0
+    nanafterend = False
+    skipzeros = False
+    minthresh = 0.0
+    maxthresh = 0.0
+    averagetypebins = "mean"
+    sortregions = "keep"
+    sortusing = "mean"
+    ortusingsamples = []
+    referencepoint = "TSS"
+    nproc = 1
+    verbose = False
+    ofile = outnpz
+
+    result = r_computematrix(
+        mode, regionlis, bwlis, sampleslabel, upstream, downstream, unscaled5prime, unscaled3prime,
+        regionbodylength, binsize, missingdatazero, metagene, txnid, exonid, txniddesignator, scale,
+        nanafterend, skipzeros, minthresh, maxthresh, averagetypebins, sortregions, sortusing,
+        ortusingsamples, referencepoint, nproc, verbose, ofile
+    )
+
+
+
+    with gzip.open(ofile, 'rb') as f:
+        file_content = f.read()
+        h = hashlib.md5(file_content).hexdigest()
+
+    expectedh = '4f1a2ce422d5b74fb6b75a81916929db'
+    assert h == expectedh
+
+    os.remove(ofile)
+
+def test_r_computematrix_scale():
+    mode = "scale-regions"
+    regionlis = [bed]
+    bwlis = [bigwig]
+    sampleslabel = ["sample1"]
+    upstream = 1000
+    downstream = 1000
+    unscaled5prime = 0
+    unscaled3prime = 0
+    regionbodylength = 0
+    binsize = 50
+    missingdatazero = False
+    metagene = False
+    txnid = ""
+    exonid = ""
+    txniddesignator = ""
+    scale = 1.0
+    nanafterend = False
+    skipzeros = False
+    minthresh = 0.0
+    maxthresh = 0.0
+    averagetypebins = "mean"
+    sortregions = "keep"
+    sortusing = "mean"
+    ortusingsamples = []
+    referencepoint = "TSS"
+    nproc = 1
+    verbose = False
+    ofile = outnpz
+
+    result = r_computematrix(
+        mode, regionlis, bwlis, sampleslabel, upstream, downstream, unscaled5prime, unscaled3prime,
+        regionbodylength, binsize, missingdatazero, metagene, txnid, exonid, txniddesignator, scale,
+        nanafterend, skipzeros, minthresh, maxthresh, averagetypebins, sortregions, sortusing,
+        ortusingsamples, referencepoint, nproc, verbose, ofile
+    )
+
+    with gzip.open(ofile, 'rb') as f:
+        file_content = f.read()
+        h = hashlib.md5(file_content).hexdigest()
+
+    
+    expectedh = '4f1a2ce422d5b74fb6b75a81916929db'
+    assert h == expectedh
+
+    os.remove(ofile)
+    

From 6fa2bd39ee27992610233a3cd1c5c54e2d8fac4f Mon Sep 17 00:00:00 2001
From: gerikson <galina.erikson@gmail.com>
Date: Wed, 22 Jan 2025 15:17:12 +0100
Subject: [PATCH 3/7] Revert "Added pytests for bamCoverage and bamCompare"

This reverts commit 7b220d3390d157c2381a34e44c82ddd169f357b4.
---
 .../deeptools/test/test_r_bamCompare.py       | 88 -------------------
 .../deeptools/test/test_r_bamCoverage.py      | 88 -------------------
 2 files changed, 176 deletions(-)
 delete mode 100644 pydeeptools/deeptools/test/test_r_bamCompare.py
 delete mode 100644 pydeeptools/deeptools/test/test_r_bamCoverage.py

diff --git a/pydeeptools/deeptools/test/test_r_bamCompare.py b/pydeeptools/deeptools/test/test_r_bamCompare.py
deleted file mode 100644
index 8749669614..0000000000
--- a/pydeeptools/deeptools/test/test_r_bamCompare.py
+++ /dev/null
@@ -1,88 +0,0 @@
-import pytest
-from deeptools.bamCompare2 import r_bamcompare
-import os.path
-import filecmp
-from os import unlink
-
-ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
-BAMFILE_A = ROOT + "test1.bam"
-BAMFILE_B = ROOT + "test2.bam"
-
-
-def test_r_bamcompare():
-    bamifile1 = BAMFILE_A
-    bamifile2 = BAMFILE_B
-    ofile = ROOT + "r_bamcompare_output.bedgraph"
-    ofiletype  = "bedgraph"
-    norm  = "None"
-    effective_genome_size = 0
-    scalefactorsmethod = "None"
-    operation = "ratio"
-    pseudocount = 0
-    # filtering options
-    ignoreduplicates = False
-    minmappingquality = 0
-    samflaginclude = 0
-    samflagexclude = 0
-    minfraglen = 0
-    maxfraglen = 0
-    nproc = 1
-    _ignorechr = []
-    binsize = 500
-    regions = []
-    verbose = False
-
-    # Call the Rust function
-    r_bamcompare(
-        bamifile1, bamifile2, ofile, ofiletype, norm, effective_genome_size, scalefactorsmethod, operation, 
-        pseudocount, ignoreduplicates, minmappingquality, samflaginclude, samflagexclude, minfraglen, maxfraglen, nproc, 
-        _ignorechr, binsize, regions, verbose
-    )
-    # Add assertions to verify the expected behavior
-    expected = ['3R\t0\t500\t0.6213592\n',
-            '3R\t500\t1000\t0.8252427\n',
-            '3R\t1000\t1500\t0.2\n',]
-    _foo = open(ofile, 'r')
-    resp = _foo.readlines()
-    _foo.close()
-    assert f"{resp}" == f"{expected}", f"{resp} != {expected}"
-    unlink(ofile)
-
-def test_r_bamcompare_RPKM():
-    bamifile1 = BAMFILE_A
-    bamifile2 = BAMFILE_B
-    ofile = ROOT + "r_bamcompare_output.bedgraph"
-    ofiletype  = "bedgraph"
-    norm  = "RPKM"
-    effective_genome_size = 0
-    scalefactorsmethod = "None"
-    operation = "ratio"
-    pseudocount = 0
-    # filtering options
-    ignoreduplicates = False
-    minmappingquality = 0
-    samflaginclude = 0
-    samflagexclude = 0
-    minfraglen = 0
-    maxfraglen = 0
-    nproc = 1
-    _ignorechr = []
-    binsize = 500
-    regions = []
-    verbose = False
-
-    # Call the Rust function
-    r_bamcompare(
-        bamifile1, bamifile2, ofile, ofiletype, norm, effective_genome_size, scalefactorsmethod, operation, 
-        pseudocount, ignoreduplicates, minmappingquality, samflaginclude, samflagexclude, minfraglen, maxfraglen, nproc, 
-        _ignorechr, binsize, regions, verbose
-    )
-    # Add assertions to verify the expected behavior
-    expected = ['3R\t0\t500\t0.6213592\n',
-            '3R\t500\t1000\t0.8252427\n',
-            '3R\t1000\t1500\t0.2\n',]
-    _foo = open(ofile, 'r')
-    resp = _foo.readlines()
-    _foo.close()
-    assert f"{resp}" == f"{expected}", f"{resp} != {expected}"
-    unlink(ofile)
\ No newline at end of file
diff --git a/pydeeptools/deeptools/test/test_r_bamCoverage.py b/pydeeptools/deeptools/test/test_r_bamCoverage.py
deleted file mode 100644
index 8749669614..0000000000
--- a/pydeeptools/deeptools/test/test_r_bamCoverage.py
+++ /dev/null
@@ -1,88 +0,0 @@
-import pytest
-from deeptools.bamCompare2 import r_bamcompare
-import os.path
-import filecmp
-from os import unlink
-
-ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
-BAMFILE_A = ROOT + "test1.bam"
-BAMFILE_B = ROOT + "test2.bam"
-
-
-def test_r_bamcompare():
-    bamifile1 = BAMFILE_A
-    bamifile2 = BAMFILE_B
-    ofile = ROOT + "r_bamcompare_output.bedgraph"
-    ofiletype  = "bedgraph"
-    norm  = "None"
-    effective_genome_size = 0
-    scalefactorsmethod = "None"
-    operation = "ratio"
-    pseudocount = 0
-    # filtering options
-    ignoreduplicates = False
-    minmappingquality = 0
-    samflaginclude = 0
-    samflagexclude = 0
-    minfraglen = 0
-    maxfraglen = 0
-    nproc = 1
-    _ignorechr = []
-    binsize = 500
-    regions = []
-    verbose = False
-
-    # Call the Rust function
-    r_bamcompare(
-        bamifile1, bamifile2, ofile, ofiletype, norm, effective_genome_size, scalefactorsmethod, operation, 
-        pseudocount, ignoreduplicates, minmappingquality, samflaginclude, samflagexclude, minfraglen, maxfraglen, nproc, 
-        _ignorechr, binsize, regions, verbose
-    )
-    # Add assertions to verify the expected behavior
-    expected = ['3R\t0\t500\t0.6213592\n',
-            '3R\t500\t1000\t0.8252427\n',
-            '3R\t1000\t1500\t0.2\n',]
-    _foo = open(ofile, 'r')
-    resp = _foo.readlines()
-    _foo.close()
-    assert f"{resp}" == f"{expected}", f"{resp} != {expected}"
-    unlink(ofile)
-
-def test_r_bamcompare_RPKM():
-    bamifile1 = BAMFILE_A
-    bamifile2 = BAMFILE_B
-    ofile = ROOT + "r_bamcompare_output.bedgraph"
-    ofiletype  = "bedgraph"
-    norm  = "RPKM"
-    effective_genome_size = 0
-    scalefactorsmethod = "None"
-    operation = "ratio"
-    pseudocount = 0
-    # filtering options
-    ignoreduplicates = False
-    minmappingquality = 0
-    samflaginclude = 0
-    samflagexclude = 0
-    minfraglen = 0
-    maxfraglen = 0
-    nproc = 1
-    _ignorechr = []
-    binsize = 500
-    regions = []
-    verbose = False
-
-    # Call the Rust function
-    r_bamcompare(
-        bamifile1, bamifile2, ofile, ofiletype, norm, effective_genome_size, scalefactorsmethod, operation, 
-        pseudocount, ignoreduplicates, minmappingquality, samflaginclude, samflagexclude, minfraglen, maxfraglen, nproc, 
-        _ignorechr, binsize, regions, verbose
-    )
-    # Add assertions to verify the expected behavior
-    expected = ['3R\t0\t500\t0.6213592\n',
-            '3R\t500\t1000\t0.8252427\n',
-            '3R\t1000\t1500\t0.2\n',]
-    _foo = open(ofile, 'r')
-    resp = _foo.readlines()
-    _foo.close()
-    assert f"{resp}" == f"{expected}", f"{resp} != {expected}"
-    unlink(ofile)
\ No newline at end of file

From 167bc6298624f3937b0d9c616b14d68713ec7422 Mon Sep 17 00:00:00 2001
From: gerikson <galina.erikson@gmail.com>
Date: Wed, 22 Jan 2025 15:23:57 +0100
Subject: [PATCH 4/7] Tests for the rust functions

---
 .../deeptools/test/test_r_bamCompare.py       |  88 +++++++++
 .../deeptools/test/test_r_bamCoverage.py      | 182 ++++++++++++++++++
 2 files changed, 270 insertions(+)
 create mode 100644 pydeeptools/deeptools/test/test_r_bamCompare.py
 create mode 100644 pydeeptools/deeptools/test/test_r_bamCoverage.py

diff --git a/pydeeptools/deeptools/test/test_r_bamCompare.py b/pydeeptools/deeptools/test/test_r_bamCompare.py
new file mode 100644
index 0000000000..84a3a660b6
--- /dev/null
+++ b/pydeeptools/deeptools/test/test_r_bamCompare.py
@@ -0,0 +1,88 @@
+import pytest
+from deeptools.bamCompare2 import r_bamcompare
+import os.path
+import filecmp
+from os import unlink
+
+ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
+BAMFILE_A = ROOT + "test1.bam"
+BAMFILE_B = ROOT + "test2.bam"
+
+
+def test_r_bamcompare():
+    bamifile1 = BAMFILE_A
+    bamifile2 = BAMFILE_B
+    ofile = ROOT + "r_bamcompare_output.bedgraph"
+    ofiletype  = "bedgraph"
+    norm  = "None"
+    effective_genome_size = 0
+    scalefactorsmethod = "None"
+    operation = "ratio"
+    pseudocount = 0
+    # filtering options
+    ignoreduplicates = False
+    minmappingquality = 0
+    samflaginclude = 0
+    samflagexclude = 0
+    minfraglen = 0
+    maxfraglen = 0
+    nproc = 1
+    _ignorechr = []
+    binsize = 500
+    regions = []
+    verbose = False
+
+    # Call the Rust function
+    r_bamcompare(
+        bamifile1, bamifile2, ofile, ofiletype, norm, effective_genome_size, scalefactorsmethod, operation, 
+        pseudocount, ignoreduplicates, minmappingquality, samflaginclude, samflagexclude, minfraglen, maxfraglen, nproc, 
+        _ignorechr, binsize, regions, verbose
+    )
+    # Add assertions to verify the expected behavior
+    expected = ['3R\t0\t500\t4.571429\n',
+            '3R\t500\t1000\t2.8333333\n',
+            '3R\t1000\t1500\t1\n',]
+    _foo = open(ofile, 'r')
+    resp = _foo.readlines()
+    _foo.close()
+    assert f"{resp}" == f"{expected}", f"{resp} != {expected}"
+    unlink(ofile)
+
+def test_r_bamcompare_RPKM():
+    bamifile1 = BAMFILE_A
+    bamifile2 = BAMFILE_B
+    ofile = ROOT + "r_bamcompare_output.bedgraph"
+    ofiletype  = "bedgraph"
+    norm  = "RPKM"
+    effective_genome_size = 0
+    scalefactorsmethod = "None"
+    operation = "ratio"
+    pseudocount = 0
+    # filtering options
+    ignoreduplicates = False
+    minmappingquality = 0
+    samflaginclude = 0
+    samflagexclude = 0
+    minfraglen = 0
+    maxfraglen = 0
+    nproc = 1
+    _ignorechr = []
+    binsize = 500
+    regions = []
+    verbose = False
+
+    # Call the Rust function
+    r_bamcompare(
+        bamifile1, bamifile2, ofile, ofiletype, norm, effective_genome_size, scalefactorsmethod, operation, 
+        pseudocount, ignoreduplicates, minmappingquality, samflaginclude, samflagexclude, minfraglen, maxfraglen, nproc, 
+        _ignorechr, binsize, regions, verbose
+    )
+    # Add assertions to verify the expected behavior
+    expected = ['3R\t0\t500\t4.571429\n',
+            '3R\t500\t1000\t2.8333333\n',
+            '3R\t1000\t1500\t1\n',]
+    _foo = open(ofile, 'r')
+    resp = _foo.readlines()
+    _foo.close()
+    assert f"{resp}" == f"{expected}", f"{resp} != {expected}"
+    unlink(ofile)
\ No newline at end of file
diff --git a/pydeeptools/deeptools/test/test_r_bamCoverage.py b/pydeeptools/deeptools/test/test_r_bamCoverage.py
new file mode 100644
index 0000000000..5d50a67ef0
--- /dev/null
+++ b/pydeeptools/deeptools/test/test_r_bamCoverage.py
@@ -0,0 +1,182 @@
+import pytest
+from deeptools.bamCoverage2 import r_bamcoverage
+import os.path
+import filecmp
+from os import unlink
+
+ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
+BAMFILE_A = ROOT + "testA.bam"
+BAMFILE_B = ROOT + "testB.bam"
+
+
+def test_r_bamcoverage():
+    bamifile = BAMFILE_A
+    ofile = ROOT + "output.bedgraph"
+    ofiletype = "bedgraph"
+    norm = "None"
+    effectivegenomesize = 0
+    scalefactor = 1.0
+    mnase = False
+    offset = [1, -1]  # Adjusted to a regular Python list
+    extendreads = 0
+    centerreads = False
+    filterrnastrand = "none"
+    blacklist = ""
+    ignorechr = []
+    skipnoncovregions = False
+    smoothlength = 0
+    binsize = 50
+    ignoreduplicates = False
+    minmappingquality = 0
+    samflaginclude = 0
+    samflagexclude = 0
+    minfraglen = 0
+    maxfraglen = 0
+    nproc = 1
+    regions = []
+    verbose = False
+
+
+    # Call the Rust function
+    r_bamcoverage(
+        bamifile, ofile, ofiletype, norm, effectivegenomesize, scalefactor, mnase, offset, extendreads, 
+        centerreads, filterrnastrand, blacklist, ignorechr, skipnoncovregions, smoothlength, 
+        binsize, ignoreduplicates, minmappingquality, samflaginclude, samflagexclude, minfraglen, maxfraglen, 
+        nproc, regions, verbose
+    )
+    # Add assertions to verify the expected behavior
+    expected = ['3R\t0\t100\t0\n', '3R\t100\t200\t1\n', 'chr_cigar\t0\t50\t1\n', 'chr_cigar\t50\t200\t0\n']
+    _foo = open(ofile, 'r')
+    resp = _foo.readlines()
+    _foo.close()
+    assert f"{resp}" == f"{expected}", f"{resp} != {expected}"
+    unlink(ofile)
+
+def test_r_bamcoverage_RPKM():
+    bamifile = BAMFILE_A
+    ofile = ROOT + "output.bedgraph"
+    ofiletype = "bedgraph"
+    norm = "RPKM"
+    effectivegenomesize = 0
+    scalefactor = 1.0
+    mnase = False
+    offset = [1, -1]  # Adjusted to a regular Python list
+    extendreads = 0
+    centerreads = False
+    filterrnastrand = "none"
+    blacklist = ""
+    ignorechr = []
+    skipnoncovregions = False
+    smoothlength = 0
+    binsize = 50
+    ignoreduplicates = False
+    minmappingquality = 0
+    samflaginclude = 0
+    samflagexclude = 0
+    minfraglen = 0
+    maxfraglen = 0
+    nproc = 1
+    regions = []
+    verbose = False
+
+
+    # Call the Rust function
+    r_bamcoverage(
+        bamifile, ofile, ofiletype, norm, effectivegenomesize, scalefactor, mnase, offset, extendreads, 
+        centerreads, filterrnastrand, blacklist, ignorechr, skipnoncovregions, smoothlength, 
+        binsize, ignoreduplicates, minmappingquality, samflaginclude, samflagexclude, minfraglen, maxfraglen, 
+        nproc, regions, verbose
+    )
+    # Add assertions to verify the expected behavior
+    expected = ['3R\t0\t100\t0\n', '3R\t100\t200\t6666666.5\n', 'chr_cigar\t0\t50\t6666666.5\n', 'chr_cigar\t50\t200\t0\n']
+    _foo = open(ofile, 'r')
+    resp = _foo.readlines()
+    _foo.close()
+    assert f"{resp}" == f"{expected}", f"{resp} != {expected}"
+    unlink(ofile)
+
+def test_r_bamcoverage_RPKM_with_effectivegenomesize():
+    bamifile = BAMFILE_B
+    ofile = ROOT + "testB.bedgraph"
+    ofiletype = "bedgraph"
+    norm = "RPKM"
+    effectivegenomesize = 142573017
+    scalefactor = 1.0
+    mnase = False
+    offset = [1, -1]  # Adjusted to a regular Python list
+    extendreads = 0
+    centerreads = False
+    filterrnastrand = "none"
+    blacklist = ""
+    ignorechr = []
+    skipnoncovregions = False
+    smoothlength = 0
+    binsize = 50
+    ignoreduplicates = False
+    minmappingquality = 0
+    samflaginclude = 0
+    samflagexclude = 0
+    minfraglen = 0
+    maxfraglen = 0
+    nproc = 1
+    regions = []
+    verbose = False
+
+
+    # Call the Rust function
+    r_bamcoverage(
+        bamifile, ofile, ofiletype, norm, effectivegenomesize, scalefactor, mnase, offset, extendreads, 
+        centerreads, filterrnastrand, blacklist, ignorechr, skipnoncovregions, smoothlength, 
+        binsize, ignoreduplicates, minmappingquality, samflaginclude, samflagexclude, minfraglen, maxfraglen, 
+        nproc, regions, verbose
+    )
+    # Add assertions to verify the expected behavior
+    expected = ['3R\t0\t50\t0\n', '3R\t50\t150\t5000000\n', '3R\t150\t200\t10000000\n']
+    _foo = open(ofile, 'r')
+    resp = _foo.readlines()
+    _foo.close()
+    assert f"{resp}" == f"{expected}", f"{resp} != {expected}"
+    unlink(ofile)
+
+def test_r_bamcoverage_RPKM_with_effectivegenomesize_and_scalefactor():
+    bamifile = BAMFILE_B
+    ofile = ROOT + "testB.bedgraph"
+    ofiletype = "bedgraph"
+    norm = "RPKM"
+    effectivegenomesize = 142573017
+    scalefactor = 2.0
+    mnase = False
+    offset = [1, -1]  # Adjusted to a regular Python list
+    extendreads = 0
+    centerreads = False
+    filterrnastrand = "none"
+    blacklist = ""
+    ignorechr = []
+    skipnoncovregions = False
+    smoothlength = 0
+    binsize = 50
+    ignoreduplicates = False
+    minmappingquality = 0
+    samflaginclude = 0
+    samflagexclude = 0
+    minfraglen = 0
+    maxfraglen = 0
+    nproc = 1
+    regions = []
+    verbose = False
+
+
+    # Call the Rust function
+    r_bamcoverage(
+        bamifile, ofile, ofiletype, norm, effectivegenomesize, scalefactor, mnase, offset, extendreads, 
+        centerreads, filterrnastrand, blacklist, ignorechr, skipnoncovregions, smoothlength, 
+        binsize, ignoreduplicates, minmappingquality, samflaginclude, samflagexclude, minfraglen, maxfraglen, 
+        nproc, regions, verbose
+    )
+    # Add assertions to verify the expected behavior
+    expected = ['3R\t0\t50\t0\n', '3R\t50\t150\t2\n', '3R\t150\t200\t4\n']
+    _foo = open(ofile, 'r')
+    resp = _foo.readlines()
+    _foo.close()
+    assert f"{resp}" == f"{expected}", f"{resp} != {expected}"
+    unlink(ofile)

From 99864de6157c6d00405b1f0bba15baa4829ee107 Mon Sep 17 00:00:00 2001
From: gerikson <galina.erikson@gmail.com>
Date: Wed, 22 Jan 2025 15:55:04 +0100
Subject: [PATCH 5/7] Tests for AlignmentSieve

---
 .../deeptools/test/test_r_alignmentsieve.py   | 133 ++++++++++++++++++
 1 file changed, 133 insertions(+)
 create mode 100644 pydeeptools/deeptools/test/test_r_alignmentsieve.py

diff --git a/pydeeptools/deeptools/test/test_r_alignmentsieve.py b/pydeeptools/deeptools/test/test_r_alignmentsieve.py
new file mode 100644
index 0000000000..55b8baa37c
--- /dev/null
+++ b/pydeeptools/deeptools/test/test_r_alignmentsieve.py
@@ -0,0 +1,133 @@
+import pytest
+from deeptools.alignmentSieve2 import r_alignmentsieve
+import os.path
+
+
+ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
+BAMFILE_A = ROOT + "test_paired.bam"
+BAMFILE_B = ROOT + "test_paired2.bam"
+
+def test_r_alignmentsieve_basic():
+    bamifile = BAMFILE_A
+    ofile = BAMFILE_B
+    nproc = 4
+    filter_metrics = ROOT + "filter_metrics_basic.txt"
+    filtered_out_readsfile = ROOT + "filtered_out_reads.bam"
+    verbose = False
+    shift = []
+    _bed = False
+    filter_rna_strand = "None"
+    min_mapping_quality = 30
+    sam_flag_incl = 0
+    sam_flag_excl = 0
+    _blacklist = ""
+    min_fragment_length = 0
+    max_fragment_length = 1000
+    extend_reads = 0
+    center_reads = False
+
+    result = r_alignmentsieve(
+        bamifile, ofile, nproc, filter_metrics, filtered_out_readsfile, verbose, shift, _bed,
+        filter_rna_strand, min_mapping_quality, sam_flag_incl, sam_flag_excl, _blacklist,
+        min_fragment_length, max_fragment_length, extend_reads, center_reads
+    )
+
+    expected_content = [
+        "#bamFilterReads --filterMetrics",
+        "#File\tReads\tRemaining Total\tInitial Reads",
+        "test_paired.bam\t49\t49"
+    ]
+
+    with open(filter_metrics, 'r') as f:
+        lines = f.readlines()
+    
+    # Remove the file path prefix from the third line
+    lines[2] = os.path.basename(lines[2])
+
+    # Strip newline characters from the lines
+    lines = [line.strip() for line in lines]
+
+    assert lines == expected_content
+
+
+def test_r_alignmentsieve_with_shift():
+    bamifile = BAMFILE_A
+    ofile = BAMFILE_B
+    nproc = 4
+    filter_metrics = ROOT + "filter_metrics_shift.txt"
+    filtered_out_readsfile = ROOT + "filtered_out_reads.bam"
+    verbose = False
+    shift = []
+    _bed = False
+    filter_rna_strand = "None"
+    min_mapping_quality = 30
+    sam_flag_incl = 0
+    sam_flag_excl = 0
+    _blacklist = ""
+    min_fragment_length = 0
+    max_fragment_length = 1000
+    extend_reads = 0
+    center_reads = False
+
+    result = r_alignmentsieve(
+        bamifile, ofile, nproc, filter_metrics, filtered_out_readsfile, verbose, shift, _bed,
+        filter_rna_strand, min_mapping_quality, sam_flag_incl, sam_flag_excl, _blacklist,
+        min_fragment_length, max_fragment_length, extend_reads, center_reads
+    )
+    
+    expected_content = [
+        "#bamFilterReads --filterMetrics",
+        "#File\tReads\tRemaining Total\tInitial Reads",
+        "test_paired.bam\t27\t49"
+    ]
+
+    with open(filter_metrics, 'r') as f:
+        lines = f.readlines()
+    
+    # Remove the file path prefix from the third line
+    lines[2] = os.path.basename(lines[2])
+
+    # Strip newline characters from the lines
+    lines = [line.strip() for line in lines]
+
+
+
+def test_r_alignmentsieve_with_filtering():
+    bamifile = BAMFILE_A
+    ofile = BAMFILE_B
+    nproc = 4
+    filter_metrics = ROOT + "filter_metrics_withFiltering.txt"
+    filtered_out_readsfile = ROOT +"filtered_out_reads.bam"
+    verbose = False
+    shift = []
+    _bed = False
+    filter_rna_strand = "forward"
+    min_mapping_quality = 30
+    sam_flag_incl = 0
+    sam_flag_excl = 0
+    _blacklist = ""
+    min_fragment_length = 100
+    max_fragment_length = 500
+    extend_reads = 0
+    center_reads = False
+
+    result = r_alignmentsieve(
+        bamifile, ofile, nproc, filter_metrics, filtered_out_readsfile, verbose, shift, _bed,
+        filter_rna_strand, min_mapping_quality, sam_flag_incl, sam_flag_excl, _blacklist,
+        min_fragment_length, max_fragment_length, extend_reads, center_reads
+    )
+    
+    expected_content = [
+        "#bamFilterReads --filterMetrics",
+        "#File\tReads\tRemaining Total\tInitial Reads",
+        "test_paired.bam\t27\t49"
+    ]
+
+    with open(filter_metrics, 'r') as f:
+        lines = f.readlines()
+    
+    # Remove the file path prefix from the third line
+    lines[2] = os.path.basename(lines[2])
+
+    # Strip newline characters from the lines
+    lines = [line.strip() for line in lines]

From b5b77df2eff59a367991ecc205c7bd033dfc4322 Mon Sep 17 00:00:00 2001
From: gerikson <galina.erikson@gmail.com>
Date: Wed, 22 Jan 2025 16:00:19 +0100
Subject: [PATCH 6/7] Fixed bug for alignment sieve

---
 pydeeptools/deeptools/test/test_r_alignmentsieve.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/pydeeptools/deeptools/test/test_r_alignmentsieve.py b/pydeeptools/deeptools/test/test_r_alignmentsieve.py
index 55b8baa37c..55572d75a7 100644
--- a/pydeeptools/deeptools/test/test_r_alignmentsieve.py
+++ b/pydeeptools/deeptools/test/test_r_alignmentsieve.py
@@ -78,7 +78,7 @@ def test_r_alignmentsieve_with_shift():
     expected_content = [
         "#bamFilterReads --filterMetrics",
         "#File\tReads\tRemaining Total\tInitial Reads",
-        "test_paired.bam\t27\t49"
+        "test_paired.bam\t49\t49"
     ]
 
     with open(filter_metrics, 'r') as f:
@@ -90,6 +90,7 @@ def test_r_alignmentsieve_with_shift():
     # Strip newline characters from the lines
     lines = [line.strip() for line in lines]
 
+    assert lines == expected_content
 
 
 def test_r_alignmentsieve_with_filtering():
@@ -131,3 +132,5 @@ def test_r_alignmentsieve_with_filtering():
 
     # Strip newline characters from the lines
     lines = [line.strip() for line in lines]
+
+    assert lines == expected_content

From 2fb3cbd28bef874b47c252ddbbcd0205d3bf9879 Mon Sep 17 00:00:00 2001
From: gerikson <galina.erikson@gmail.com>
Date: Wed, 22 Jan 2025 16:10:32 +0100
Subject: [PATCH 7/7] Fixed bug for alignment sieve

---
 .../deeptools/test/test_r_alignmentsieve.py   | 42 +++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/pydeeptools/deeptools/test/test_r_alignmentsieve.py b/pydeeptools/deeptools/test/test_r_alignmentsieve.py
index 55572d75a7..de031b244b 100644
--- a/pydeeptools/deeptools/test/test_r_alignmentsieve.py
+++ b/pydeeptools/deeptools/test/test_r_alignmentsieve.py
@@ -134,3 +134,45 @@ def test_r_alignmentsieve_with_filtering():
     lines = [line.strip() for line in lines]
 
     assert lines == expected_content
+
+def test_r_alignmentsieve_with_filtering_extendReads():
+    bamifile = BAMFILE_A
+    ofile = BAMFILE_B
+    nproc = 4
+    filter_metrics = ROOT + "filter_metrics_extendReads.txt"
+    filtered_out_readsfile = ROOT +"filtered_out_reads.bam"
+    verbose = False
+    shift = []
+    _bed = False
+    filter_rna_strand = "forward"
+    min_mapping_quality = 30
+    sam_flag_incl = 0
+    sam_flag_excl = 0
+    _blacklist = ""
+    min_fragment_length = 100
+    max_fragment_length = 500
+    extend_reads = 100
+    center_reads = False
+
+    result = r_alignmentsieve(
+        bamifile, ofile, nproc, filter_metrics, filtered_out_readsfile, verbose, shift, _bed,
+        filter_rna_strand, min_mapping_quality, sam_flag_incl, sam_flag_excl, _blacklist,
+        min_fragment_length, max_fragment_length, extend_reads, center_reads
+    )
+    
+    expected_content = [
+        "#bamFilterReads --filterMetrics",
+        "#File\tReads\tRemaining Total\tInitial Reads",
+        "test_paired.bam\t27\t49"
+    ]
+
+    with open(filter_metrics, 'r') as f:
+        lines = f.readlines()
+    
+    # Remove the file path prefix from the third line
+    lines[2] = os.path.basename(lines[2])
+
+    # Strip newline characters from the lines
+    lines = [line.strip() for line in lines]
+
+    assert lines == expected_content