Changeset 4290

Timestamp:

Feb 3, 2023, 4:17:58 PM (4 months ago)

Author:

Peter

Message:

add same interface for program_group as for read_group in class BamHeader?.

Location:

trunk

Files:

• test/bam_header.cc (modified) (3 diffs)
• yat/omic/BamHeader.cc (modified) (5 diffs)
• yat/omic/BamHeader.h (modified) (2 diffs)

trunk/test/bam_header.cc

@@ -23 +23 @@
 #include "yat/omic/BamFile.h"
 #include "yat/omic/BamHeader.h"
+#include <set>
 #endif
+
 
 using namespace theplu::yat;
@@ -172 +174 @@
   int32_t n_chr = hdr.n_targets();
 
-  // check that we can add another chromosomevia a @SG field
+  // check that we can add another chromosome via a @SG field
   std::stringstream ss(hdr.text());
   std::string str3;
@@ -253 +255 @@
     suite.out() << "expected exception with what(): " << e.what() << "\n";
   }
+
+
+  std::set<std::string>
+    programs(hdr.program_group_begin(), hdr.program_group_end());
+  for (const auto& prog : programs)
+    suite.out() << prog << "\n";
+  if (!programs.count("bwa") || !programs.count("samtools") ||
+      programs.size()!=3) {
+    suite.add(false);
+    suite.err() << "incorrect programs\n";
+  }
+  hdr.program_group("bwa");
 }
 #endif

trunk/yat/omic/BamHeader.cc

@@ -67 +67 @@
 
 
+  const std::map<std::string, std::string>&
+  BamHeader::group(strMap2& map, const std::string& type,
+                   const std::string& id) const
+  {
+    update_group(map, type);
+    strMap2::const_iterator line_table = map.find(id);
+    if (line_table == map.end()) {
+      std::string msg = "@" + type + ": unknown ID: '" + id + "'";
+      throw utility::runtime_error(msg);
+    }
+    return line_table->second;
+  }
+
+
+  BamHeader::read_group_iterator
+  BamHeader::group_begin(strMap2& group, const std::string& type) const
+  {
+    update_group(group, type);
+    BamHeader::strMap2::const_iterator it(group.begin());
+    return utility::pair_first_iterator(it);
+  }
+
+
+  BamHeader::read_group_iterator
+  BamHeader::group_end(strMap2& group, const std::string& type) const
+  {
+    update_group(group, type);
+    BamHeader::strMap2::const_iterator it(group.end());
+    return utility::pair_first_iterator(it);
+  }
+
+
   const std::string& BamHeader::group(strMap2& table,const std::string& type,
                                       const std::string& id,
                                       const std::string& key) const
   {
-    update_group(table, type);
-    strMap2::const_iterator line_table = table.find(id);
-    if (line_table == table.end()) {
-      std::string msg = "@" + type + ": unknown ID: '" + id + "'";
-      throw utility::runtime_error(msg);
-    }
-    strMap::const_iterator it = line_table->second.find(key);
-    if (it == line_table->second.end()) {
+    const std::map<std::string, std::string>& m = group(table, type, id);
+    strMap::const_iterator it = m.find(key);
+    if (it == m.end()) {
       std::string msg = "@" + type + ": unknown KEY: '" + key + "'";
       throw utility::runtime_error(msg);
@@ -142 +169 @@
 
 
+  const std::map<std::string, std::string>&
+  BamHeader::program_group(const std::string& id) const
+  {
+    return group(program_group_, "PG", id);
+  }
+
+
+  BamHeader::program_group_iterator BamHeader::program_group_begin(void) const
+  {
+    return group_begin(program_group_, "PG");
+  }
+
+
+  BamHeader::program_group_iterator BamHeader::program_group_end(void) const
+  {
+    return group_end(program_group_, "PG");
+  }
+
+
   const std::string& BamHeader::read_group(const std::string& id,
                                            const std::string& key) const
@@ -152 +198 @@
   BamHeader::read_group(const std::string& id) const
   {
-    update_group(read_group_, "RG");
-    strMap2::const_iterator line_table = read_group_.find(id);
-    if (line_table == read_group_.end()) {
-      std::string msg = "@RG: unknown ID: '" + id + "'";
-      throw utility::runtime_error(msg);
-    }
-    return line_table->second;
+    return group(read_group_, "RG", id);
   }
 
@@ -164 +204 @@
   BamHeader::read_group_iterator BamHeader::read_group_begin(void) const
   {
-    update_group(read_group_, "RG");
-    BamHeader::strMap2::const_iterator it(read_group_.begin());
-    return utility::pair_first_iterator(it);
+    return group_begin(read_group_, "RG");
   }
 
@@ -172 +210 @@
   BamHeader::read_group_iterator BamHeader::read_group_end(void) const
   {
-    update_group(read_group_, "RG");
-    BamHeader::strMap2::const_iterator it(read_group_.end());
-    return utility::pair_first_iterator(it);
+    return group_end(read_group_, "RG");
   }
 

trunk/yat/omic/BamHeader.h

@@ -106 +106 @@
 
     /**
+       \returns a map describing an \@PG line such as
+
+       \code @PG  ID:bwa  PN:bwa  VN:0.6.1-r104 \endcode
+
+       for which the returned map contains two entries: one with key
+       \c PN and value \c bwa, and one with key \c VN and value
+       \c 0.6.1-r104.
+
+       \since New in yat 0.21
+     */
+    const std::map<std::string, std::string>&
+    program_group(const std::string& id) const;
+
+    /**
+       program_group_iterator is used to iterate through program groups
+
+       program_group_iterator is a \readable_iterator and
+       \bidirectional_traversal_iterator with value type \c
+       std::string
+
+       \see program_group_begin
+       \see program_group_end
+
+       \since New in yat 0.21
+     */
+    typedef boost::transform_iterator<
+      utility::PairFirst<const strMap2::value_type>,
+      strMap2::const_iterator>
+    program_group_iterator;
+
+    /**
+       \return first of available PG IDs
+
+       \since New in yat 0.21
+     */
+    program_group_iterator program_group_begin(void) const;
+
+    /**
+       \return end of range of available PG IDs
+
+       \see program_group_begin()
+
+       \since New in yat 0.21
+     */
+    program_group_iterator program_group_end(void) const;
+
+    /**
        \brief Access value in \c \@RG lines.
 
@@ -240 +287 @@
     friend class OutBamFile;
 
+    const std::map<std::string, std::string>&
+    group(strMap2&, const std::string& type,
+          const std::string& id) const;
+
+    read_group_iterator
+    group_begin(strMap2&, const std::string& type) const;
+
+    read_group_iterator
+    group_end(strMap2&, const std::string& type) const;
+
     const std::string& group(strMap2& map, const std::string& type,
                              const std::string& id,