diff --git a/galaxy/wrapper/bamCompare.xml b/galaxy/wrapper/bamCompare.xml
index 6e654af427..0e012b5747 100644
--- a/galaxy/wrapper/bamCompare.xml
+++ b/galaxy/wrapper/bamCompare.xml
@@ -198,7 +198,7 @@
             <param name="type" value="ratio"/>
             <output name="outFileName" file="bamCompare_result2.bw" ftype="bigwig"/>
         </test>
-        <!-- Test with BAM and CRAM file as input-->
+        <!-- Test with BAM and CRAM file as input
         <test expect_num_outputs="1">
             <param name="bamFile1" value="testA.bam" ftype="bam"/>
             <param name="bamFile2" value="testA.cram" ftype="cram"/>
@@ -212,8 +212,8 @@
                     <has_text_matching expression="chr_cigar\t0\t200\t1"/>
                 </assert_contents>
             </output>
-        </test>
-        <!-- Test with BAM and CRAM files and substract option-->
+        </test> -->
+        <!-- Test with BAM and CRAM files and substract option. This is disabled for now.
         <test expect_num_outputs="1">
             <param name="bamFile1" value="testA.bam" ftype="bam"/>
             <param name="bamFile2" value="testA.cram" ftype="cram"/>
@@ -227,7 +227,7 @@
                     <has_text_matching expression="chr_cigar\t0\t200\t0"/>
                 </assert_contents>
             </output>
-        </test>
+        </test> -->
         <!-- Test with BAM files with pseudocounts-->
         <test expect_num_outputs="1">
             <param name="bamFile1" value="testA.bam" ftype="bam"/>
@@ -240,9 +240,9 @@
             <output name="outFileName" ftype="bedgraph">
                 <assert_contents>
                     <has_text_matching expression="3R\t0\t50\t1"/>
-                    <has_text_matching expression="3R\t50\t100\t0.571429"/>
-                    <has_text_matching expression="3R\t100\t150\t1.14286"/>
-                    <has_text_matching expression="3R\t150\t200\t0.8"/>
+                    <has_text_matching expression="3R\t50\t100\t0.67"/>
+                    <has_text_matching expression="3R\t100\t150\t1.33"/>
+                    <has_text_matching expression="3R\t150\t200\t1"/>
                 </assert_contents>
             </output>
         </test>
@@ -257,9 +257,9 @@
             <param name="skipZeroOverZero" value="--skipZeroOverZero"/>
             <output name="outFileName" ftype="bedgraph">
                 <assert_contents>
-                    <has_text_matching expression="3R\t50\t100\t0.571429"/>
-                    <has_text_matching expression="3R\t100\t150\t1.14286"/>
-                    <has_text_matching expression="3R\t150\t200\t0.8"/>
+                    <has_text_matching expression="3R\t50\t100\t0.67"/>
+                    <has_text_matching expression="3R\t100\t150\t1.33"/>
+                    <has_text_matching expression="3R\t150\t200\t1"/>
                 </assert_contents>
             </output>
         </test>
@@ -274,8 +274,8 @@
             <param name="skipNAs" value="true"/>
             <output name="outFileName" ftype="bedgraph">
                 <assert_contents>
-                    <has_text_matching expression="3R\t100\t150\t1.14286"/>
-                    <has_text_matching expression="3R\t150\t200\t0.8"/>
+                    <has_text_matching expression="3R\t100\t150\t1.33"/>
+                    <has_text_matching expression="3R\t150\t200\t1"/>
                 </assert_contents>
             </output>
         </test>
diff --git a/galaxy/wrapper/test-data/bamCompare_result2.bw b/galaxy/wrapper/test-data/bamCompare_result2.bw
index d6d5c0438b..75b87e5000 100644
Binary files a/galaxy/wrapper/test-data/bamCompare_result2.bw and b/galaxy/wrapper/test-data/bamCompare_result2.bw differ
diff --git a/galaxy/wrapper/test-data/bamCoverage_result1.bw b/galaxy/wrapper/test-data/bamCoverage_result1.bw
index d489b05384..695105d378 100644
Binary files a/galaxy/wrapper/test-data/bamCoverage_result1.bw and b/galaxy/wrapper/test-data/bamCoverage_result1.bw differ
diff --git a/galaxy/wrapper/test-data/bamCoverage_result2.bw b/galaxy/wrapper/test-data/bamCoverage_result2.bw
index 70ef6dd0cc..846ed84a57 100644
Binary files a/galaxy/wrapper/test-data/bamCoverage_result2.bw and b/galaxy/wrapper/test-data/bamCoverage_result2.bw differ
diff --git a/galaxy/wrapper/test-data/bamCoverage_result3.bg b/galaxy/wrapper/test-data/bamCoverage_result3.bg
index 1e0793e5c2..25cf375b05 100644
--- a/galaxy/wrapper/test-data/bamCoverage_result3.bg
+++ b/galaxy/wrapper/test-data/bamCoverage_result3.bg
@@ -1,7 +1,7 @@
-chrM	0	210	9.76876e+06
-chrM	210	220	9.56092e+06
-chrM	220	230	7.6903e+06
-chrM	230	240	5.19615e+06
-chrM	240	250	3.32554e+06
-chrM	250	260	623538
+chrM	0	210	9768765
+chrM	210	220	9560919
+chrM	220	230	7690304.5
+chrM	230	240	5196151.5
+chrM	240	250	3325537
+chrM	250	260	623538.2
 chrM	260	16569	0
diff --git a/galaxy/wrapper/test-data/bamCoverage_result4.bg b/galaxy/wrapper/test-data/bamCoverage_result4.bg
index 24b6f0c3c7..ded2d121f4 100644
--- a/galaxy/wrapper/test-data/bamCoverage_result4.bg
+++ b/galaxy/wrapper/test-data/bamCoverage_result4.bg
@@ -1,472 +1,472 @@
-phiX174	0	10	16038.5
-phiX174	10	20	48115.4
-phiX174	20	70	144346
-phiX174	70	80	192462
-phiX174	80	90	176423
-phiX174	90	100	160385
-phiX174	100	120	112269
-phiX174	120	140	144346
-phiX174	140	150	160385
-phiX174	150	160	128308
-phiX174	160	170	160385
-phiX174	170	180	176423
+phiX174	0	10	16038.46
+phiX174	10	20	48115.39
+phiX174	20	70	144346.16
+phiX174	70	80	192461.55
+phiX174	80	90	176423.08
+phiX174	90	100	160384.63
+phiX174	100	120	112269.23
+phiX174	120	140	144346.16
+phiX174	140	150	160384.63
+phiX174	150	160	128307.7
+phiX174	160	170	160384.63
+phiX174	170	180	176423.08
 phiX174	180	200	208500
-phiX174	200	210	192462
-phiX174	210	220	240577
-phiX174	220	230	272654
-phiX174	230	240	336808
-phiX174	240	250	320769
-phiX174	250	260	288692
-phiX174	260	270	336808
-phiX174	270	280	400962
+phiX174	200	210	192461.55
+phiX174	210	220	240576.92
+phiX174	220	230	272653.84
+phiX174	230	240	336807.7
+phiX174	240	250	320769.25
+phiX174	250	260	288692.3
+phiX174	260	270	336807.7
+phiX174	270	280	400961.56
 phiX174	280	300	417000
-phiX174	300	310	352846
-phiX174	310	320	320769
-phiX174	320	330	368885
-phiX174	330	340	352846
-phiX174	340	350	288692
-phiX174	350	360	256615
-phiX174	360	370	224538
-phiX174	370	380	240577
-phiX174	380	390	304731
-phiX174	390	400	256615
-phiX174	400	410	240577
-phiX174	410	420	224538
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+phiX174	300	310	352846.16
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+phiX174	340	350	288692.3
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+phiX174	360	370	224538.45
+phiX174	370	380	240576.92
+phiX174	380	390	304730.78
+phiX174	390	400	256615.4
+phiX174	400	410	240576.92
+phiX174	410	420	224538.45
+phiX174	420	450	288692.3
+phiX174	450	460	304730.78
+phiX174	460	470	336807.7
 phiX174	470	490	417000
-phiX174	490	510	497192
-phiX174	510	520	465115
-phiX174	520	530	561346
-phiX174	530	540	497192
-phiX174	540	550	529269
-phiX174	550	560	545308
-phiX174	560	570	641538
+phiX174	490	510	497192.3
+phiX174	510	520	465115.4
+phiX174	520	530	561346.2
+phiX174	530	540	497192.3
+phiX174	540	550	529269.25
+phiX174	550	560	545307.7
+phiX174	560	570	641538.5
 phiX174	570	580	625500
-phiX174	580	590	561346
-phiX174	590	600	609462
-phiX174	600	610	545308
+phiX174	580	590	561346.2
+phiX174	590	600	609461.56
+phiX174	600	610	545307.7
 phiX174	610	630	625500
-phiX174	630	640	577385
-phiX174	640	650	513231
-phiX174	650	660	545308
-phiX174	660	670	561346
-phiX174	670	680	593423
-phiX174	680	690	657577
-phiX174	690	700	641538
-phiX174	700	710	561346
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-phiX174	730	740	513231
-phiX174	740	760	593423
-phiX174	760	770	497192
-phiX174	770	780	513231
-phiX174	780	790	529269
-phiX174	790	800	545308
-phiX174	800	810	449077
-phiX174	810	820	433038
-phiX174	820	830	368885
-phiX174	830	840	320769
-phiX174	840	850	352846
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-phiX174	870	880	256615
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-phiX174	890	900	384923
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-phiX174	940	950	577385
-phiX174	950	960	593423
-phiX174	960	970	513231
-phiX174	970	980	481154
-phiX174	980	990	433038
+phiX174	630	640	577384.6
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+phiX174	770	780	513230.8
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+phiX174	800	810	449076.9
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+phiX174	820	830	368884.63
+phiX174	830	840	320769.25
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+phiX174	850	860	304730.78
+phiX174	860	870	336807.7
+phiX174	870	880	256615.4
+phiX174	880	890	352846.16
+phiX174	890	900	384923.1
+phiX174	900	910	465115.4
+phiX174	910	920	545307.7
+phiX174	920	930	561346.2
+phiX174	930	940	545307.7
+phiX174	940	950	577384.6
+phiX174	950	960	593423.06
+phiX174	960	970	513230.8
+phiX174	970	980	481153.84
+phiX174	980	990	433038.47
 phiX174	990	1000	417000
-phiX174	1000	1010	449077
-phiX174	1010	1030	577385
-phiX174	1030	1040	753808
-phiX174	1040	1050	785885
-phiX174	1050	1060	817962
-phiX174	1060	1070	866077
+phiX174	1000	1010	449076.9
+phiX174	1010	1030	577384.6
+phiX174	1030	1040	753807.7
+phiX174	1040	1050	785884.6
+phiX174	1050	1060	817961.6
+phiX174	1060	1070	866076.94
 phiX174	1070	1080	834000
-phiX174	1080	1090	866077
-phiX174	1090	1100	769846
-phiX174	1100	1110	737769
-phiX174	1110	1120	657577
-phiX174	1120	1130	641538
+phiX174	1080	1090	866076.94
+phiX174	1090	1100	769846.2
+phiX174	1100	1110	737769.25
+phiX174	1110	1120	657576.94
+phiX174	1120	1130	641538.5
 phiX174	1130	1140	625500
-phiX174	1140	1150	673615
+phiX174	1140	1150	673615.4
 phiX174	1150	1160	625500
-phiX174	1160	1170	593423
-phiX174	1170	1180	609462
-phiX174	1180	1190	577385
-phiX174	1190	1200	513231
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-phiX174	1210	1220	561346
-phiX174	1220	1230	481154
-phiX174	1230	1240	449077
-phiX174	1240	1250	352846
-phiX174	1250	1260	336808
-phiX174	1260	1270	400962
-phiX174	1270	1280	352846
-phiX174	1280	1290	368885
-phiX174	1290	1300	320769
-phiX174	1300	1310	384923
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-phiX174	1330	1340	513231
-phiX174	1340	1350	481154
-phiX174	1350	1370	497192
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-phiX174	1390	1400	352846
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-phiX174	1410	1430	481154
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-phiX174	1490	1500	545308
-phiX174	1500	1510	657577
+phiX174	1160	1170	593423.06
+phiX174	1170	1180	609461.56
+phiX174	1180	1190	577384.6
+phiX174	1190	1200	513230.8
+phiX174	1200	1210	481153.84
+phiX174	1210	1220	561346.2
+phiX174	1220	1230	481153.84
+phiX174	1230	1240	449076.9
+phiX174	1240	1250	352846.16
+phiX174	1250	1260	336807.7
+phiX174	1260	1270	400961.56
+phiX174	1270	1280	352846.16
+phiX174	1280	1290	368884.63
+phiX174	1290	1300	320769.25
+phiX174	1300	1310	384923.1
+phiX174	1310	1320	513230.8
+phiX174	1320	1330	497192.3
+phiX174	1330	1340	513230.8
+phiX174	1340	1350	481153.84
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+phiX174	1470	1480	609461.56
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+phiX174	1490	1500	545307.7
+phiX174	1500	1510	657576.94
 phiX174	1510	1520	625500
-phiX174	1520	1540	785885
-phiX174	1540	1550	721731
-phiX174	1550	1570	753808
-phiX174	1570	1580	769846
-phiX174	1580	1590	673615
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+phiX174	1570	1580	769846.2
+phiX174	1580	1590	673615.4
 phiX174	1590	1600	625500
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+phiX174	1730	1740	577384.6
+phiX174	1740	1750	529269.25
+phiX174	1750	1760	433038.47
 phiX174	1760	1770	417000
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-phiX174	1790	1810	336808
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-phiX174	1880	1890	673615
-phiX174	1890	1900	705692
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-phiX174	1960	1970	529269
-phiX174	1970	1980	673615
-phiX174	1980	1990	641538
-phiX174	1990	2000	657577
-phiX174	2000	2010	673615
-phiX174	2010	2020	641538
-phiX174	2020	2030	657577
-phiX174	2030	2050	673615
-phiX174	2050	2060	481154
-phiX174	2060	2070	513231
-phiX174	2070	2080	481154
-phiX174	2080	2100	513231
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-phiX174	2120	2130	529269
-phiX174	2130	2140	545308
-phiX174	2140	2150	513231
-phiX174	2150	2160	545308
+phiX174	1770	1780	368884.63
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+phiX174	1790	1810	336807.7
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+phiX174	1830	1860	705692.3
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+phiX174	1870	1880	737769.25
+phiX174	1880	1890	673615.4
+phiX174	1890	1900	705692.3
+phiX174	1900	1910	609461.56
+phiX174	1910	1920	400961.56
+phiX174	1920	1930	465115.4
+phiX174	1930	1940	545307.7
+phiX174	1940	1950	449076.9
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+phiX174	1960	1970	529269.25
+phiX174	1970	1980	673615.4
+phiX174	1980	1990	641538.5
+phiX174	1990	2000	657576.94
+phiX174	2000	2010	673615.4
+phiX174	2010	2020	641538.5
+phiX174	2020	2030	657576.94
+phiX174	2030	2050	673615.4
+phiX174	2050	2060	481153.84
+phiX174	2060	2070	513230.8
+phiX174	2070	2080	481153.84
+phiX174	2080	2100	513230.8
+phiX174	2100	2110	529269.25
+phiX174	2110	2120	513230.8
+phiX174	2120	2130	529269.25
+phiX174	2130	2140	545307.7
+phiX174	2140	2150	513230.8
+phiX174	2150	2160	545307.7
 phiX174	2160	2170	417000
-phiX174	2170	2180	352846
-phiX174	2180	2190	433038
-phiX174	2190	2200	449077
-phiX174	2200	2210	433038
-phiX174	2210	2220	481154
-phiX174	2220	2230	545308
-phiX174	2230	2240	593423
+phiX174	2170	2180	352846.16
+phiX174	2180	2190	433038.47
+phiX174	2190	2200	449076.9
+phiX174	2200	2210	433038.47
+phiX174	2210	2220	481153.84
+phiX174	2220	2230	545307.7
+phiX174	2230	2240	593423.06
 phiX174	2240	2250	625500
-phiX174	2250	2260	721731
+phiX174	2250	2260	721730.8
 phiX174	2260	2270	625500
-phiX174	2270	2290	593423
-phiX174	2290	2300	609462
-phiX174	2300	2310	737769
-phiX174	2310	2320	769846
-phiX174	2320	2330	866077
-phiX174	2330	2340	850038
-phiX174	2340	2350	898154
-phiX174	2350	2360	801923
-phiX174	2360	2370	914192
-phiX174	2370	2380	801923
-phiX174	2380	2390	641538
-phiX174	2390	2400	593423
+phiX174	2270	2290	593423.06
+phiX174	2290	2300	609461.56
+phiX174	2300	2310	737769.25
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+phiX174	5220	5230	400961.56
+phiX174	5230	5240	449076.9
+phiX174	5240	5250	368884.63
+phiX174	5250	5260	272653.84
+phiX174	5260	5270	304730.78
+phiX174	5270	5280	336807.7
+phiX174	5280	5290	272653.84
+phiX174	5290	5300	192461.55
+phiX174	5300	5310	144346.16
+phiX174	5310	5340	96230.77
+phiX174	5340	5350	64153.85
+phiX174	5350	5386	32076.93
diff --git a/galaxy/wrapper/test-data/bamCoverage_result4.bw b/galaxy/wrapper/test-data/bamCoverage_result4.bw
index 6eb0b982ac..82ee20c0b6 100644
Binary files a/galaxy/wrapper/test-data/bamCoverage_result4.bw and b/galaxy/wrapper/test-data/bamCoverage_result4.bw differ
diff --git a/galaxy/wrapper/test-data/bamCoverage_result5.bw b/galaxy/wrapper/test-data/bamCoverage_result5.bw
index fba54ecc8a..cfd82515c7 100644
Binary files a/galaxy/wrapper/test-data/bamCoverage_result5.bw and b/galaxy/wrapper/test-data/bamCoverage_result5.bw differ
diff --git a/galaxy/wrapper/test-data/bamCoverage_result6.bw b/galaxy/wrapper/test-data/bamCoverage_result6.bw
index c4676fe2fc..969d8052a5 100644
Binary files a/galaxy/wrapper/test-data/bamCoverage_result6.bw and b/galaxy/wrapper/test-data/bamCoverage_result6.bw differ
diff --git a/galaxy/wrapper/test-data/coverage_filtered.bg b/galaxy/wrapper/test-data/coverage_filtered.bg
index 4448c0afb8..30e2ccbe9f 100644
--- a/galaxy/wrapper/test-data/coverage_filtered.bg
+++ b/galaxy/wrapper/test-data/coverage_filtered.bg
@@ -1,19 +1,19 @@
-3R	0	50	0.295172
-3R	50	100	0.885515
-3R	100	150	2.21379
-3R	150	250	4.87034
-3R	250	300	3.0993
-3R	300	350	2.36137
-3R	350	400	2.21379
-3R	400	450	3.54206
-3R	450	500	4.13241
-3R	500	550	2.0662
-3R	550	600	2.50896
-3R	600	650	4.57516
-3R	650	700	3.24689
-3R	700	750	3.39448
-3R	750	800	3.83723
-3R	900	950	1.91862
-3R	950	1000	1.32827
-3R	1000	1050	0.73793
+3R	0	50	0.33
+3R	50	100	1
+3R	100	150	2.5
+3R	150	250	5.49
+3R	250	300	3.49
+3R	300	350	2.66
+3R	350	400	2.5
+3R	400	450	3.99
+3R	450	500	4.66
+3R	500	550	2.33
+3R	550	600	2.83
+3R	600	650	5.16
+3R	650	750	3.66
+3R	750	800	2.5
+3R	800	900	0
+3R	900	950	0.5
+3R	950	1000	1.33
+3R	1000	1050	0.83
 3R	1050	1500	0
diff --git a/galaxy/wrapper/test-data/plotCorrelation_result1.png b/galaxy/wrapper/test-data/plotCorrelation_result1.png
index a0f7558e93..c2373582bb 100644
Binary files a/galaxy/wrapper/test-data/plotCorrelation_result1.png and b/galaxy/wrapper/test-data/plotCorrelation_result1.png differ
diff --git a/galaxy/wrapper/test-data/plotCorrelation_result1.tabular b/galaxy/wrapper/test-data/plotCorrelation_result1.tabular
index 16d9470a65..524a3a25c6 100644
--- a/galaxy/wrapper/test-data/plotCorrelation_result1.tabular
+++ b/galaxy/wrapper/test-data/plotCorrelation_result1.tabular
@@ -1,4 +1,3 @@
-#plotCorrelation --outFileCorMatrix
 	'bowtie2 test1.bam'	'bowtie2 test1.bam'
 'bowtie2 test1.bam'	1.0000	1.0000
 'bowtie2 test1.bam'	1.0000	1.0000
diff --git a/galaxy/wrapper/test-data/plotPCA_result2.png b/galaxy/wrapper/test-data/plotPCA_result2.png
index ad0ee26656..f2feec050e 100644
Binary files a/galaxy/wrapper/test-data/plotPCA_result2.png and b/galaxy/wrapper/test-data/plotPCA_result2.png differ
diff --git a/galaxy/wrapper/test-data/plotPCA_result2.tabular b/galaxy/wrapper/test-data/plotPCA_result2.tabular
index ebdc6ff748..3ae66a2321 100644
--- a/galaxy/wrapper/test-data/plotPCA_result2.tabular
+++ b/galaxy/wrapper/test-data/plotPCA_result2.tabular
@@ -1,4 +1,3 @@
-#plotPCA --outFileNameData
 Component	bowtie2-test1.bam	bowtie2-test1.bam	Eigenvalue
-1	-0.7071067811865476	-0.7071067811865475	4.0
-2	-0.7071067811865475	0.7071067811865476	1.2325951644078315e-32
+1	1.9994942044176225	0.0	2.9999999999999996
+2	-0.9607959164084681	0.0	0.0
diff --git a/galaxy/wrapper/test-data/profiler_result1.png b/galaxy/wrapper/test-data/profiler_result1.png
index 6bdfb4adaf..2cdfba2255 100644
Binary files a/galaxy/wrapper/test-data/profiler_result1.png and b/galaxy/wrapper/test-data/profiler_result1.png differ
diff --git a/pydeeptools/deeptools/bamCoverage2.py b/pydeeptools/deeptools/bamCoverage2.py
index b8fd97ffce..deac6d428a 100644
--- a/pydeeptools/deeptools/bamCoverage2.py
+++ b/pydeeptools/deeptools/bamCoverage2.py
@@ -144,8 +144,15 @@ def main(args=None):
         args.normalizeUsing = 'None'
     if not args.Offset:
         args.Offset = [0, 0]
+    # in rust, no offset is encoded as 0,0
+    # in python code 1, -1 corresponds to no offset.
     elif len(args.Offset) == 1:
         args.Offset = [args.Offset[0], 0]
+    else:
+        if args.Offset[1] == -1:
+            args.Offset[1] = 0
+        args.Offset = [args.Offset[0], args.Offset[1]]
+
     if not args.extendReads:
         args.extendReads = False
         args.extendReadsLen = 0
diff --git a/pyproject.toml b/pyproject.toml
index 61d0af858f..c218cb5687 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -63,20 +63,20 @@ repository = "https://github.com/deeptools/deepTools"
 packages = ["deeptools"]
 
 [project.scripts]
-#alignmentSieve = "deeptools.alignmentSieve:main"
-#bamCompare = "deeptools.bamCompare:main"
-#bamCoverage = "deeptools.bamCoverage:main"
+alignmentSieve = "deeptools.alignmentSieve:main"
+#bamCompare_old = "deeptools.bamCompare:main"
+#bamCoverage_old = "deeptools.bamCoverage:main"
 bamPEFragmentSize = "deeptools.bamPEFragmentSize:main"
 bigwigAverage = "deeptools.bigwigAverage:main"
 bigwigCompare = "deeptools.bigwigCompare:main"
 computeGCBias = "deeptools.computeGCBias:main"
-#computeMatrix = "deeptools.computeMatrix:main"
+#computeMatrix_old = "deeptools.computeMatrix:main"
 computeMatrixOperations = "deeptools.computeMatrixOperations:main"
 correctGCBias = "deeptools.correctGCBias:main"
 deeptools = "deeptools.deeptools_list_tools:main"
 estimateReadFiltering = "deeptools.estimateReadFiltering:main"
 estimateScaleFactor = "deeptools.estimateScaleFactor:main"
-#multiBamSummary = "deeptools.multiBamSummary:main"
+#multiBamSummary_old = "deeptools.multiBamSummary:main"
 multiBigwigSummary = "deeptools.multiBigwigSummary:main"
 plotCorrelation = "deeptools.plotCorrelation:main"
 plotCoverage = "deeptools.plotCoverage:main"
@@ -88,5 +88,5 @@ plotProfile = "deeptools.plotProfile:main"
 bamCoverage = "deeptools.bamCoverage2:main"
 bamCompare = "deeptools.bamCompare2:main"
 computeMatrix = "deeptools.computeMatrix2:main"
-alignmentSieve = "deeptools.alignmentSieve2:main"
+#alignmentSieve = "deeptools.alignmentSieve2:main"
 multiBamSummary = "deeptools.multiBamSummary2:main"