BAM Review Action Items - Revision history

Ppwhite: /* Accessing String Values */

2017-02-02T16:01:04Z

Accessing String Values

← Older revision		Revision as of 12:01, 2 February 2017
Line 158:		Line 158:
	</source>		</source>

	http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/html/SamRecord_8h-source.html		http://csg.sph.umich.edu//mktrost/doxygen/html/SamRecord_8h-source.html

	==== SamFileHeader ====		==== SamFileHeader ====

Ppwhite: /* Useful Links */

2017-02-02T15:06:26Z

Useful Links

← Older revision		Revision as of 11:06, 2 February 2017
Line 30:		Line 30:
	BAM Library FAQs: http://genome.sph.umich.edu/wiki/SAM/BAM_Library_FAQs		BAM Library FAQs: http://genome.sph.umich.edu/wiki/SAM/BAM_Library_FAQs

	Source Code: http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/html/		Source Code: http://csg.sph.umich.edu//mktrost/doxygen/html/

	Test code for setting values in the library: http://~~www~~.sph.umich.edu/~~csg~~/mktrost/doxygen/html/WriteFiles_8cpp-source.html		Test code for setting values in the library: http://csg.sph.umich.edu//mktrost/doxygen/html/WriteFiles_8cpp-source.html

	=== Topics for Discussion ===		=== Topics for Discussion ===

Mktrost: /* Review June 7th */

2010-12-09T22:55:31Z

Review June 7th

← Older revision		Revision as of 18:55, 9 December 2010
Line 205:		Line 205:
	** <S>include links from the main library page and the SamFile page.</s>		** <S>include links from the main library page and the SamFile page.</s>
	** <S>look into why the one example have two if checks on SamIn status</s> <span style="color:blue">- one was printing the result and one was setting the return value - cleaned up to be in one if statement.</span>		** <S>look into why the one example have two if checks on SamIn status</s> <span style="color:blue">- one was printing the result and one was setting the return value - cleaned up to be in one if statement.</span>
	* Create 1 library for all of our library code rather than having libcsg, libbam, libfqf separated.		* <S>Create 1 library for all of our library code rather than having libcsg, libbam, libfqf separated.</s>
	** What should this library be called?		** <S>What should this library be called?</s> <span style="color:blue">- Created library: libstatgen and reorganized into a new repository: statgen.</span>
	*** libdna		*** <S>libdna</s>
	*** libdna++		*** <S>libdna++</s>
	*** libsequence++		*** <S>libsequence++</s>
	*** libDNA		*** <S>libDNA</s>
	*** libgenotype		*** <S>libgenotype</s>
	* Add an option by class that says whether or not to abort on failure. (or even an option on each method)		* Add an option by class that says whether or not to abort on failure. (or even an option on each method)
	** This allows calling code to set that option and then not have to check for failures since the code it calls would abort on a failure.		** This allows calling code to set that option and then not have to check for failures since the code it calls would abort on a failure.

Mktrost at 05:47, 2 November 2010

2010-11-02T05:47:41Z

← Older revision		Revision as of 01:47, 2 November 2010
Line 1:		Line 1:
			[[Category:libStatGen]]
			[[Category:libStatGen BAM]]

	== Review Sept 20th ==		== Review Sept 20th ==
	=== Notes ===		=== Notes ===

Mktrost: /* Notes */

2010-09-20T18:55:30Z

Notes

← Older revision		Revision as of 14:55, 20 September 2010
Line 3:		Line 3:
	* returning const char*		* returning const char*
	* SamFileHeader change referenceContigs, etc to private from public		* SamFileHeader change referenceContigs, etc to private from public
			* Add way to copy a SAM record.

	== Review Sept 17th ==		== Review Sept 17th ==

Mktrost at 18:45, 20 September 2010

2010-09-20T18:45:39Z

← Older revision		Revision as of 14:45, 20 September 2010
Line 1:		Line 1:
	== Review Sept 20th ==		== Review Sept 20th ==
	=== Notes ===		=== Notes ===
			* returning const char*
			* SamFileHeader change referenceContigs, etc to private from public

	== Review Sept 17th ==		== Review Sept 17th ==

Mktrost: /* Accessing String Values */

2010-09-20T18:25:56Z

Accessing String Values

@@ Line 103: / Line 103: @@
      return mySequence.c_str();
+}
 </source>
 and passing in references to strings, like:

Mktrost at 18:10, 20 September 2010

2010-09-20T18:10:12Z

← Older revision		Revision as of 14:10, 20 September 2010
Line 1:		Line 1:
			== Review Sept 20th ==
			=== Notes ===

	== Review Sept 17th ==		== Review Sept 17th ==
	=== Topics Discussed ===		=== Topics Discussed ===

Mktrost: /* NOTES From Meeting */

2010-09-17T19:42:30Z

NOTES From Meeting

← Older revision		Revision as of 15:42, 17 September 2010
Line 14:		Line 14:
	** Problems with passing in std::string& as a parameter to be set.		** Problems with passing in std::string& as a parameter to be set.
	*** people typically want to operate on the return of the method.		*** people typically want to operate on the return of the method.
			** One idea was returning a reference to a string
			*** Does that solve the problem? Won't the contents change when a new one is read? Is that what we want?

	==== Useful Links ====
			=== Useful Links ===
	BAM Library FAQs: http://genome.sph.umich.edu/wiki/SAM/BAM_Library_FAQs		BAM Library FAQs: http://genome.sph.umich.edu/wiki/SAM/BAM_Library_FAQs

Mktrost at 19:30, 17 September 2010

2010-09-17T19:30:19Z

@@ Line 5: / Line 5: @@
 === NOTES From Meeting ===
-*InputFile should not use <code>long int</code>.  Should instead use: <code>long long</code>
+* General Notes:
-*Anytime have an error could call handleError which would have a switch to return the error, throw exception, or abort.  Call it with an error code and a string.  Maybe an error handler class where you could use everywhere.  Each class would have a member of that class type that would contain that information.
+**InputFile should not use <code>long int</code>.  Should instead use: <code>long long</code>
 ==== Useful Links ====
@@ Line 88: / Line 95: @@
          setSequenceAndQualityFromBuffer();
+     }
      return mySequence.c_str();
+}