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fix complication warnings
USe default second column (1-based) for tables JIRA GP-35948
1-based column numbers JIRA GP-35948
Option for including uniprot source comment JIRA GP-35948
when resuming taskrun, take into account whether last execution was interrupted cleanly JIRA GP-35746
option for getting sequence taxids for FASTA as a separate input JIRA GP-35725
flag for non-exclusive execution JIRA GP-32676
apply chunk file size limit JIRA GP-32153
correct output seq-ids when id-prefix is used JIRA GP-32156
Disable parsing sequence ranges JIRA RW-1437
Replaced auto_ptr with unique_ptr. JIRA CXX-11620
Make caching resumable for FASTA and SRA JIRA GP-29671
Introducing strict TTaxId. JIRA CXX-10489
Fixed TEntrezId usage. JIRA CXX-10489
Use CFastaReader message listener that tolerates unrecognized modifier names JIRA GP-28177
fix -Wreorder warning
revert r585406
fix -Wreorder warnings
override molinfo more intelligently; JIRA: PGAP-1062
check pointers; JIRA: PGAP-909
squash -Wreorder
prime_cache gently treats descriptors that came from CFastaReader; JIRA: PGAP-909 - added m_Genome state - added m_Orgref state - treatment of molinfo and biosource descriptors is refactored. -- apply genome wide orgref and genome only when the descriptor has undefined enum value on it or non-existent - previous (siltent) bug fixed for m_other_descs
added more one-per-list descriptors to the select using a list provided by Colleen on JIRA: PGAP-858
for a selected list of descriptors, do not append, but try to replace first; JIRA: PGAP-858 - added upsert API - registered list of upsertable descriptors: source, molinfo for now
Modified to use local_taxon. JIRA: GP-24223
Option to add bioseq descriptor parameters for SRA data JIRA GP-23803
Option in caching FASTA to specify seq-id length limits JIRA CXX-9968
In csra more output should look as usual, seq-ids of cached sequences JIRA GP-3823
JIRA:GP-19297. Fix compilation warnings.
JIRA:GP-17063. Clean up compiler warnings.
Workaround CFastaReader bug in implementation of fNoUserObjs flag JIRA GP-15746
Don't create raw defline User-object when reading Fasta JIRA GP-15746
Formally take advantage of recently implemented support for using the WGS data loader where available and otherwise managing without it. (This change doesn't affect behavior on platforms with VDB available, just allows for best-effort functionality elsewhere. In the long term, some or all of these apps may want to adopt CDataLoadersUtil, as already done by asnvalidate.) JIRA: CXX-8143, SQD-1776.
extract-delta option JIRA GP-17460
Moved asn_cache apps into app/asn_cache. JIRA: CXX-8143
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