| /dports/biology/bbmap/bbmap/current/var2/ |
| H A D | Realign.java | 83 samFilter.includeUnmapped=false; in Realign()
84 samFilter.includeSupplimentary=false; in Realign()
85 samFilter.includeDuplicate=true; in Realign()
86 samFilter.includeNonPrimary=true; in Realign()
87 samFilter.includeQfail=false; in Realign()
88 samFilter.minMapq=4; in Realign()
125 else if(samFilter.parse(arg, a, b)){ in Realign()
138 samFilter.setSamtoolsFilter(); in Realign()
197 ScafMap.loadReference(ref, scafMap, samFilter, true); in loadReference()
429 if(samFilter!=null && !samFilter.passesFilter(sl)){return false;}
[all …]
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| H A D | FilterVCF.java | 106 samFilter.clear(); in FilterVCF()
108 }else if(samFilter.parse(arg, a, b)){ in FilterVCF()
138 if(!setSamFilter){samFilter=null;} in FilterVCF()
167 if(ref!=null){ScafMap.loadReference(ref, scafMap, samFilter, true);} in FilterVCF()
329 if(pass && samFilter!=null){pass&=samFilter.passesFilter(vline);} in processVcfVarsST()
581 if(pass && samFilter!=null){pass&=samFilter.passesFilter(vline);} in processLine()
664 SamFilter samFilter=new SamFilter(); field in FilterVCF
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| H A D | ScafMap.java | 88 …public static ScafMap loadReference(String fname, ScafMap scafMap, SamFilter samFilter, boolean ma… in loadReference() argument
90 return loadReference(ff, scafMap, samFilter, makeDefault); in loadReference()
93 …public static ScafMap loadReference(FileFormat ff, ScafMap map, SamFilter samFilter, boolean makeD… in loadReference() argument
98 if(samFilter==null || samFilter.passesFilter(r.id)){ in loadReference()
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| H A D | CallVariants2.java | 97 samFilter.includeUnmapped=false; in CallVariants2()
98 samFilter.includeSupplimentary=false; in CallVariants2()
99 samFilter.includeDuplicate=false; in CallVariants2()
100 samFilter.includeNonPrimary=false; in CallVariants2()
101 samFilter.includeQfail=false; in CallVariants2()
102 samFilter.minMapq=4; in CallVariants2()
195 else if(samFilter.parse(arg, a, b)){ in CallVariants2()
216 samFilter.clear(); in CallVariants2()
252 samFilter.setSamtoolsFilter(); in CallVariants2()
1074 if(samFilter!=null && !samFilter.passesFilter(sl)){return false;} in processRead()
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| H A D | CallVariants.java | 126 samFilter.includeUnmapped=false; in CallVariants()
127 samFilter.includeSupplimentary=false; in CallVariants()
128 samFilter.includeDuplicate=false; in CallVariants()
129 samFilter.includeNonPrimary=false; in CallVariants()
130 samFilter.includeQfail=false; in CallVariants()
131 samFilter.minMapq=4; in CallVariants()
243 else if(samFilter.parse(arg, a, b)){ in CallVariants()
264 samFilter.clear(); in CallVariants()
300 samFilter.setSamtoolsFilter(); in CallVariants()
1116 if(samFilter!=null && !samFilter.passesFilter(sl)){return false;} in processRead()
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| /dports/biology/bbmap/bbmap/current/consensus/ |
| H A D | FixScaffoldGaps.java | 81 samFilter.includeUnmapped=false; in FixScaffoldGaps()
82 samFilter.includeSupplimentary=false; in FixScaffoldGaps()
84 samFilter.includeNonPrimary=false; in FixScaffoldGaps()
85 samFilter.includeQfail=false; in FixScaffoldGaps()
107 samFilter.setSamtoolsFilter(); in FixScaffoldGaps()
168 samFilter.clear(); in parse()
173 }else if(samFilter.parse(arg, a, b)){ in parse()
519 if(samFilter!=null && !samFilter.passesFilter(sl)){return;} in processRead()
736 public final SamFilter samFilter=new SamFilter(); field in FixScaffoldGaps
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| H A D | Lilypad.java | 82 samFilter.includeUnmapped=false; in Lilypad()
83 samFilter.includeSupplimentary=false; in Lilypad()
85 samFilter.includeNonPrimary=false; in Lilypad()
86 samFilter.includeQfail=false; in Lilypad()
87 samFilter.minMapq=4; in Lilypad()
108 samFilter.setSamtoolsFilter(); in Lilypad()
174 samFilter.clear(); in parse()
179 }else if(samFilter.parse(arg, a, b)){ in parse()
537 if(samFilter!=null && !samFilter.passesFilter(sl)){return;} in processRead()
957 public final SamFilter samFilter=new SamFilter(); field in Lilypad
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| H A D | ConsensusMaker.java | 84 samFilter.includeUnmapped=false; in ConsensusMaker()
87 samFilter.includeNonPrimary=false; in ConsensusMaker()
88 samFilter.includeQfail=false; in ConsensusMaker()
113 samFilter.setSamtoolsFilter(); in ConsensusMaker()
215 samFilter.clear(); in parse()
220 }else if(samFilter.parse(arg, a, b)){ in parse()
713 if(samFilter!=null && !samFilter.passesFilter(sl)){return;}
849 public final SamFilter samFilter=new SamFilter(); local
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| /dports/biology/bbmap/bbmap/current/template/ |
| H A D | A_SampleSamStreamer.java | 106 samFilter.setSamtoolsFilter(); in A_SampleSamStreamer()
161 samFilter.clear(); in parse()
166 }else if(samFilter.parse(arg, a, b)){ in parse()
281 scafMap=ScafMap.loadReference(ref, scafMap, samFilter, true);
455 if(samFilter!=null && !samFilter.passesFilter(sl)){return false;}
533 public final SamFilter samFilter=new SamFilter(); local
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