cleaned up __ prefixes. removed blat from master branch

walaj · Oct 5, 2016 · 00a80e5 · 00a80e5
1 parent 2d68be2
commit 00a80e5
Show file tree

Hide file tree

Showing 21 changed files with 74 additions and 1,480 deletions.
diff --git a/SeqLib/BFC.h b/SeqLib/BFC.h
@@ -1,5 +1,5 @@
-#ifndef SEQLIB_BFC_H__
-#define SEQLIB_BFC_H__
+#ifndef SEQLIB_BFC_H
+#define SEQLIB_BFC_H
 
 extern "C" {
   #include "fermi-lite/bfc.h"

diff --git a/SeqLib/BLATWrapper.h b/SeqLib/BLATWrapper.h
diff --git a/SeqLib/BWAWrapper.h b/SeqLib/BWAWrapper.h
@@ -1,5 +1,5 @@
-#ifndef SEQLIB_BWAWRAPPER_H__
-#define SEQLIB_BWAWRAPPER_H__
+#ifndef SEQLIB_BWAWRAPPER_H
+#define SEQLIB_BWAWRAPPER_H
 
 #include <string>
 #include <vector>
@@ -173,19 +173,19 @@ class BWAWrapper {
   std::string bwa_print_sam_hdr2(const bntseq_t *bns, const char *hdr_line) const;
 
   // overwrite the bwa bwt_pac2pwt function
-  bwt_t *__bwt_pac2bwt(const uint8_t *pac, int bwt_seq_lenr);
+  bwt_t *seqlib_bwt_pac2bwt(const uint8_t *pac, int bwt_seq_lenr);
 
   // add an anns (chr annotation structure) 
-  bntann1_t* __add_to_anns(const std::string& name, const std::string& seq, bntann1_t * ann, size_t offset);
+  bntann1_t* seqlib_add_to_anns(const std::string& name, const std::string& seq, bntann1_t * ann, size_t offset);
 
   // overwrite the bwa-mem add1 function, which takes a sequence and adds to pac
-  uint8_t* __add1(const kseq_t *seq, bntseq_t *bns, uint8_t *pac, int64_t *m_pac, int *m_seqs, int *m_holes, bntamb1_t **q);
+  uint8_t* seqlib_add1(const kseq_t *seq, bntseq_t *bns, uint8_t *pac, int64_t *m_pac, int *m_seqs, int *m_holes, bntamb1_t **q);
 
   // make the pac structure (2-bit encoded packed sequence)
-  uint8_t* __make_pac(const UnalignedSequenceVector& v, bool for_only);
+  uint8_t* seqlib_make_pac(const UnalignedSequenceVector& v, bool for_only);
 
   // write pac part of the index
-  void __write_pac_to_file(const std::string& file) const;
+  void seqlib_write_pac_to_file(const std::string& file) const;
 
   // write the bns file of the index
   std::string print_bns();

diff --git a/SeqLib/BamReader.h b/SeqLib/BamReader.h
@@ -1,5 +1,5 @@
-#ifndef SEQLIB_BAM_POLYREADER_H__
-#define SEQLIB_BAM_POLYREADER_H__
+#ifndef SEQLIB_BAM_POLYREADER_H
+#define SEQLIB_BAM_POLYREADER_H
 
 #include <cassert>
 #include "SeqLib/ReadFilter.h"
@@ -42,7 +42,7 @@ namespace SeqLib {
   private:
 
     // do the read loading
-    bool __load_read(BamRecord& r);
+    bool load_read(BamRecord& r);
 
     void reset() {
       empty = true;

diff --git a/SeqLib/BamRecord.h b/SeqLib/BamRecord.h
@@ -1,5 +1,5 @@
-#ifndef SEQLIB_BAM_RECORD_H__
-#define SEQLIB_BAM_RECORD_H__
+#ifndef SEQLIB_BAM_RECORD_H
+#define SEQLIB_BAM_RECORD_H
 
 #include <stdint.h>
 //#include <cstdint> //+11

diff --git a/SeqLib/BamWriter.h b/SeqLib/BamWriter.h
@@ -1,5 +1,5 @@
-#ifndef SEQLIB_BAM_WRITER_H__
-#define SEQLIB_BAM_WRITER_H__
+#ifndef SEQLIB_BAM_WRITER_H
+#define SEQLIB_BAM_WRITER_H
 
 #include <cassert>
 #include "SeqLib/BamRecord.h"
@@ -94,7 +94,7 @@ class BamWriter  {
   std::string m_out; 
 
   // open m_out, true if success
-  void __open_BAM_for_writing();
+  void open_BAM_for_writing();
 
   // output format
   std::string output_format; 

diff --git a/SeqLib/FastqReader.h b/SeqLib/FastqReader.h
@@ -1,5 +1,5 @@
-#ifndef SEQLIB_FASTQ_READER_H__
-#define SEQLIB_FASTQ_READER_H__
+#ifndef SEQLIB_FASTQ_READER_H
+#define SEQLIB_FASTQ_READER_H
 
 #include <string>
 

diff --git a/SeqLib/FermiAssembler.h b/SeqLib/FermiAssembler.h
@@ -1,5 +1,5 @@
-#ifndef SEQLIB_FERMI_H__
-#define SEQLIB_FERMI_H__
+#ifndef SEQLIB_FERMI_H
+#define SEQLIB_FERMI_H
 
 #include <string>
 #include <cstdlib>

diff --git a/SeqLib/GenomicRegionCollection.cpp b/SeqLib/GenomicRegionCollection.cpp
@@ -19,7 +19,7 @@ namespace SeqLib {
   GenomicRegionCollection<T>::GenomicRegionCollection(int width, int ovlp, const HeaderSequenceVector& h) {
 
     idx = 0;
-    __allocate_grc();
+    allocate_grc();
 
     // undefined otherwise
     if (width <= ovlp)
@@ -298,7 +298,7 @@ bool GenomicRegionCollection<T>::ReadVCF(const std::string & file, const BamHead
 template<class T>
 GenomicRegionCollection<T>::GenomicRegionCollection(const std::string &file, const BamHeader& hdr) {
 
-  __allocate_grc();
+  allocate_grc();
 
   idx = 0;
 
@@ -418,7 +418,7 @@ template<class T>
 GenomicRegionCollection<T>::GenomicRegionCollection(int width, int ovlp, const T &gr) {
 
   idx = 0;
-  __allocate_grc();
+  allocate_grc();
 
   // undefined otherwise
   if (width <= ovlp)
@@ -546,7 +546,7 @@ void GenomicRegionCollection<T>::Concat(const GenomicRegionCollection<T>& g)
 template<class T>
 GenomicRegionCollection<T>::GenomicRegionCollection() {
   idx = 0;
-  __allocate_grc();
+  allocate_grc();
 }
 
 template<class T>
@@ -555,7 +555,7 @@ GenomicRegionCollection<T>::~GenomicRegionCollection() {
 
 
 template<class T>
-void GenomicRegionCollection<T>::__allocate_grc() {
+void GenomicRegionCollection<T>::allocate_grc() {
   m_sorted = false;
   m_grv =  SeqPointer<std::vector<T> >(new std::vector<T>()) ;
   m_tree = SeqPointer<GenomicIntervalTreeMap>(new GenomicIntervalTreeMap()) ;
@@ -565,7 +565,7 @@ template<class T>
 GenomicRegionCollection<T>::GenomicRegionCollection(const BamRecordVector& brv) {
   idx = 0;
 
-  __allocate_grc();
+  allocate_grc();
 
   //for (auto& i : brv) 
   for (BamRecordVector::const_iterator i = brv.begin(); i != brv.end(); ++i) 
@@ -726,7 +726,7 @@ GenomicRegionCollection<T>::GenomicRegionCollection(const T& gr)
 {
   m_sorted = true;
   idx = 0;
-  __allocate_grc();
+  allocate_grc();
   m_grv->push_back(gr);
 }
 

diff --git a/SeqLib/GenomicRegionCollection.h b/SeqLib/GenomicRegionCollection.h
@@ -1,5 +1,5 @@
-#ifndef SWAP_GENOMIC_REGION_COLLECTION_H__
-#define SWAP_GENOMIC_REGION_COLLECTION_H__
+#ifndef SWAP_GENOMIC_REGION_COLLECTION_H
+#define SWAP_GENOMIC_REGION_COLLECTION_H
 
 #include <vector>
 #include <string>
@@ -291,7 +291,7 @@ class GenomicRegionCollection {
  size_t idx;
 
  // open the memory
- void __allocate_grc();
+ void allocate_grc();
 
 };
 

diff --git a/SeqLib/ReadFilter.h b/SeqLib/ReadFilter.h
@@ -1,5 +1,5 @@
-#ifndef SEQLIB_READ_FILTER_H__
-#define SEQLIB_READ_FILTER_H__
+#ifndef SEQLIB_READ_FILTER_H
+#define SEQLIB_READ_FILTER_H
 
 #define AHO_CORASICK 1
 
@@ -256,7 +256,7 @@ class FlagRule {
   uint32_t m_any_on_flag; // if read has any of these, keep
   uint32_t m_any_off_flag;// if read has any of these, fail
 
-  int __parse_json_int(const Json::Value& v);
+  int parse_json_int(const Json::Value& v);
 
 };
 
@@ -548,7 +548,6 @@ class ReadFilterCollection {
 
   bool ParseFilterObject(const std::string& filterName, const Json::Value& filterObject);
 
-  //bool __validate_json_value(const Json::Value value);
 };
 
 }

diff --git a/SeqLib/RefGenome.h b/SeqLib/RefGenome.h
@@ -1,5 +1,5 @@
-#ifndef SEQLIB_REF_GENOME_H__
-#define SEQLIB_REF_GENOME_H__
+#ifndef SEQLIB_REF_GENOME_H
+#define SEQLIB_REF_GENOME_H
 
 #include <string>
 #include <cstdlib>

diff --git a/SeqLib/SeqLibCommon.h b/SeqLib/SeqLibCommon.h
@@ -1,5 +1,5 @@
-#ifndef SEQLIB_COMMON_H__
-#define SEQLIB_COMMON_H__
+#ifndef SEQLIB_COMMON_H
+#define SEQLIB_COMMON_H
 
 /*! \mainpage SeqLib 1.0
  *