add mate0 and mate1 readSequence
make up related functions in readHeadSet
comment the genomix-data temporally, will recover later
use VKmerList to replace the EdgeMap
change edgeType in Node
change graph building to adapt new ray style
tweak graphviz
change function name of node from getEdgeMap to getEdgeList
Merge commit '1b7005d5a2f185c29ea677f4246a4889d805fa36' into nanzhang/ray-genomix

# By Jake Biesinger
# Via Jake Biesinger
* commit '1b7005d5a2f185c29ea677f4246a4889d805fa36':
  remove garbage GAGETEST.fasta
  fix scaffolding bug where incomingMsg details weren't included
  explicitly set the length to 0 at the beginning of BFS
  fix BubbleMerge bug where an incorrect major/minor to bubble dir was used
  use null for default values in all pregelix messages
  stopgap fix for pathmerge problem introduced by #51 in commit 447146c

Conflicts:
	genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/message/BubbleMergeMessage.java
	genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/message/PathMergeMessage.java
Merge branch 'genomix/fullstack_genomix' into nanzhang/ray-genomix

# By buyingyi (16) and others
# Via ecarm002@ucr.edu (8) and others
* genomix/fullstack_genomix: (41 commits)
  update to new pregelix aggregator interface
  fix application lifecyle mgmt in hyracks nc
  fix the pinned page issue during a node failure
  Make sure the validty bit in the metadata page is flushed to disk when marking a component to be valid.
  NodeControllers clean up appEntryPoints on shutdown (2nd try)
  fix an issue found by Sattam
  Fix for issue 127.
  minor fix for heartbeat state population
  support multiple user-defined global aggregators
  reverted the change of removing adjacent exchange operators
  updated hivestrix test case for running aggregation fix
  Fixed a bug on unclosed running aggregation runtime; fixed an issue on two adjacent exchange operators (connectors) when duplicate sort operator is removed.
  Fixed the incorrect exchange merging introduced by the previous commit; updated the IntroHashPartitionMergeExchange rule to handle the hash-merge-exchange operator.
  Fixed a bug on omitted order by columns when added an exchange operator to enforce the group-by property.
  Fixed a bug on unclosed running aggregation runtime; fixed an issue on two adjacent exchange operators (connectors) when duplicate sort operator is removed.
  revert a minor change
  revert a minor change
  fix IIndexAccessor interface, add a boolean exclusiveMode parameter for the createSearchCursor method
  fix file write race condition
  Revert changes to InlineVariablesRule.
  ...
change this/thatSequence, and bitField for not writing any null members
change SetAsCopy() and getLengthInBytes() to be consistent with writing nothing about null members
remove contain(Kmer kmer) and recover contain(VkmerList kmer)
change partial member function to be consistent with ReadHeadInfo
get mateId in a indirect way, and consider the single long end read
Merge branch 'genomix/fullstack_genomix' into nanzhang/ray-genomix

# By Jake Biesinger
# Via Jake Biesinger
* genomix/fullstack_genomix:
  fix for null value in GraphStatistics
  set coverage in split repeat to 1/2 the node's coverage
  udpate hyracks test cases to use null's
  Node uses null values and writes less to stream
  use <enum>.values() instead of EnumSet.allOf()

Conflicts:
	genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/Node.java
	genomix/genomix-data/src/test/java/edu/uci/ics/genomix/type/NodeTest.java
	genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/AggregateKmerAggregateFactory.java
	genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
change setAsCopy() to use getThisReadSequence() and getThatReadSequence()
use getKmerLetterLength() instead of getKmerBytesLength()
check toString() in readHeadInfo
change getEdgeList() to getEdgeMap() in readKeyValueParser