### BAM Test Case: Small Reference Region with Start Offset

Source: https://github.com/ncbi/ncbi-cxx-toolkit-public/blob/main/src/sra/readers/bam/test/CMakeLists.bam_test.app.txt

Configures a test case for the bam_test application to read a small reference region with a start offset, checking a specific count of records.

```cmake
NCBI_begin_test(bam_test4)
    NCBI_set_test_command(bam_test -refseq GL000207.1 -refpos 50 -refwindow 100 -by-start -check_count 1)
  NCBI_end_test()
```

--------------------------------

### BAM Test Application Setup

Source: https://github.com/ncbi/ncbi-cxx-toolkit-public/blob/main/src/sra/readers/bam/test/CMakeLists.bam_test.app.txt

Sets up the bam_test application, defining its sources, dependencies, and watchers.

```cmake
NCBI_begin_app(bam_test)
  NCBI_sources(bam_test bam_test_common)
  NCBI_uses_toolkit_libraries(bamread xobjreadex xobjsimple)
  NCBI_project_watchers(vasilche ucko)

  NCBI_set_test_requires(full-test-data)
```

--------------------------------

### BAM Test Case: Specific Reference Region with Start Offset

Source: https://github.com/ncbi/ncbi-cxx-toolkit-public/blob/main/src/sra/readers/bam/test/CMakeLists.bam_test.app.txt

Configures a test case for the bam_test application to read a specific reference sequence and region with a start offset, checking a specific count of records.

```cmake
NCBI_begin_test(bam_test2)
    NCBI_set_test_command(bam_test -file NA10851.chrom20.ILLUMINA.bwa.CEU.low_coverage.20111114.bam -refseq 20 -refpos 100000 -refwindow 100000 -by-start -check_count 15215)
  NCBI_end_test()
```

--------------------------------

### CMakeLists.txt Configuration for BLAST Unit Tests

Source: https://github.com/ncbi/ncbi-cxx-toolkit-public/blob/main/src/algo/blast/unit_tests/api/CMakeLists.txt

This snippet configures the CMake build system for BLAST API unit tests. It includes directives for setting up include paths, definitions, and adding numerous test applications.

```cmake
# $Id$

NCBI_requires(Boost.Test.Included)
NCBI_add_include_directories(${NCBI_CURRENT_SOURCE_DIR}/../../api)
NCBI_add_definitions(NCBI_MODULE=BLAST)
NCBI_add_library(blast_unit_test_util seqalign_util)

NCBI_add_app(
  blast_unit_test
  aalookup_unit_test
  seqsrc_unit_test
  delta_unit_test
  ntlookup_unit_test
  seqinfosrc_unit_test
  setupfactory_unit_test
  search_strategy_unit_test
  redoalignment_unit_test
  queryinfo_unit_test
  querydata_unit_test
  pssmenginefreqratios_unit_test
  blastsetup_unit_test
  blastextend_unit_test
  blastdiag_unit_test
  pssmcreate_unit_test
  psiblast_iteration_unit_test
  hspfilter_besthit_unit_test
  hspfilter_culling_unit_test
  optionshandle_unit_test
  msa2pssm_unit_test
  tracebacksearch_unit_test
  traceback_unit_test
  psibl2seq_unit_test
  psiblast_unit_test
  prelimsearch_unit_test
  phiblast_unit_test
  split_query_unit_test
  scoreblk_unit_test
  hspstream_unit_test
  rps_unit_test
  gapinfo_unit_test
  blasthits_unit_test
  linkhsp_unit_test
  blastengine_unit_test
  subj_ranges_unit_test
  version_reference_unit_test
  ntscan_unit_test
  aascan_unit_test
  remote_blast_unit_test
  uniform_search_unit_test
  blastfilter_unit_test
  blastoptions_unit_test
  gencode_singleton_unit_test
  bl2seq_unit_test
  stat_unit_test
  magicblast_unit_test
  rmblast_blasthits_unit_test
  rmblast_traceback_unit_test
)

```

--------------------------------

### BAM Test Case: No Records Expected (Reference and Header Only)

Source: https://github.com/ncbi/ncbi-cxx-toolkit-public/blob/main/src/sra/readers/bam/test/CMakeLists.bam_test.app.txt

Configures a test case for the bam_test application to check for zero records when specifying both reference parameters and a header-only file.

```cmake
NCBI_begin_test(bam_test_q_none2)
    NCBI_set_test_command(bam_test -file header-only.bam -refseq GL000207.1 -refwindow 1 -check_count 0)
  NCBI_end_test()
```

--------------------------------

### BAM Test Case: No Records Expected (Reference)

Source: https://github.com/ncbi/ncbi-cxx-toolkit-public/blob/main/src/sra/readers/bam/test/CMakeLists.bam_test.app.txt

Configures a test case for the bam_test application where no records are expected based on reference parameters, checking for zero count.

```cmake
NCBI_begin_test(bam_test_none)
    NCBI_set_test_command(bam_test -refseq GL000207.1 -refwindow 1 -check_count 0)
  NCBI_end_test()
```

--------------------------------

### BAM Test Case: No Records Expected (Header Only File)

Source: https://github.com/ncbi/ncbi-cxx-toolkit-public/blob/main/src/sra/readers/bam/test/CMakeLists.bam_test.app.txt

Configures a test case for the bam_test application to check for zero records in a header-only BAM file.

```cmake
NCBI_begin_test(bam_test_none3)
    NCBI_set_test_command(bam_test -file header-only.bam -check_count 0)
  NCBI_end_test()
```

--------------------------------

### BAM Test Case: Default Index

Source: https://github.com/ncbi/ncbi-cxx-toolkit-public/blob/main/src/sra/readers/bam/test/CMakeLists.bam_test.app.txt

Configures a test case for the bam_test application to run with default indexing, checking a specific count of records.

```cmake
NCBI_begin_test(bam_test_no_index1)
    NCBI_set_test_command(bam_test -file NA10851.chrom20.ILLUMINA.bwa.CEU.low_coverage.20111114.bam -check_count 100000)
  NCBI_end_test()
```

--------------------------------

### Configure BAM Graph Test Application

Source: https://github.com/ncbi/ncbi-cxx-toolkit-public/blob/main/src/sra/readers/bam/test/CMakeLists.bamgraph_test.app.txt

Defines the application name, sources, and required NCBI toolkit libraries for the bamgraph_test application.

```cmake
# $Id$

NCBI_begin_app(bamgraph_test)
  NCBI_sources(bamgraph_test)
  NCBI_uses_toolkit_libraries(bamread)
  NCBI_project_watchers(vasilche ucko)
NCBI_end_app()

```

--------------------------------

### Add netschedule Applications

Source: https://github.com/ncbi/ncbi-cxx-toolkit-public/blob/main/src/sample/app/netschedule/CMakeLists.txt

This snippet uses the NCBI_add_app macro to define a list of netschedule-related applications to be built by CMake.

```cmake
NCBI_add_app(
  netschedule_client_sample 
  netschedule_node_sample
  grid_worker_sample 
  grid_client_sample 
  grid_cgi_sample
  rcgi_sample 
  remote_app_client_sample 
)
```

--------------------------------

### BAM Test Case: No Records Expected (Reference and Unaligned)

Source: https://github.com/ncbi/ncbi-cxx-toolkit-public/blob/main/src/sra/readers/bam/test/CMakeLists.bam_test.app.txt

Configures a test case for the bam_test application to check for zero records when specifying both reference parameters and an unaligned file.

```cmake
NCBI_begin_test(bam_test_q_none)
    NCBI_set_test_command(bam_test -file 1k.unaligned.bam -refseq GL000207.1 -refwindow 1 -check_count 0)
  NCBI_end_test()
```

--------------------------------

### BAM Test Case: No Records Expected (Unaligned File)

Source: https://github.com/ncbi/ncbi-cxx-toolkit-public/blob/main/src/sra/readers/bam/test/CMakeLists.bam_test.app.txt

Configures a test case for the bam_test application to check for zero records in an unaligned BAM file.

```cmake
NCBI_begin_test(bam_test_none2)
    NCBI_set_test_command(bam_test -file 1k.unaligned.bam -check_count 0)
  NCBI_end_test()
```

--------------------------------

### BAM Test Case: Small Reference Region

Source: https://github.com/ncbi/ncbi-cxx-toolkit-public/blob/main/src/sra/readers/bam/test/CMakeLists.bam_test.app.txt

Configures a test case for the bam_test application to read a small reference region, checking a specific count of records.

```cmake
NCBI_begin_test(bam_test3)
    NCBI_set_test_command(bam_test -refseq GL000207.1 -refpos 50 -refwindow 100 -check_count 2)
  NCBI_end_test()
```

--------------------------------

### BAM Test Case: No Index

Source: https://github.com/ncbi/ncbi-cxx-toolkit-public/blob/main/src/sra/readers/bam/test/CMakeLists.bam_test.app.txt

Configures a test case for the bam_test application to run without an index, checking a specific count of records.

```cmake
NCBI_begin_test(bam_test_no_index0)
    NCBI_set_test_command(bam_test -file NA10851.chrom20.ILLUMINA.bwa.CEU.low_coverage.20111114.bam -no_index -check_count 100000)
  NCBI_end_test()
```

--------------------------------

### BAM Test Case: Specific Reference Region

Source: https://github.com/ncbi/ncbi-cxx-toolkit-public/blob/main/src/sra/readers/bam/test/CMakeLists.bam_test.app.txt

Configures a test case for the bam_test application to read a specific reference sequence and region, checking a specific count of records.

```cmake
NCBI_begin_test(bam_test)
    NCBI_set_test_command(bam_test -file NA10851.chrom20.ILLUMINA.bwa.CEU.low_coverage.20111114.bam -refseq 20 -refpos 100000 -refwindow 100000 -check_count 15219)
  NCBI_end_test()
```

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