[med-svn] [Git][med-team/biobambam2][master] 2 commits: Fix errors in autopkgtests

[Pranav Ballaney]

Pranav Ballaney pushed to branch master at Debian Med / biobambam2


Commits:
53a4c9b8 by Pranav Ballaney at 2020-05-27T19:35:07+05:30
Fix errors in autopkgtests

- - - - -
8f789457 by Pranav Ballaney at 2020-05-27T19:35:27+05:30
Move examples to another binary package

- - - - -


4 changed files:

- + debian/biobambam2-examples.install
- debian/control
- debian/docs
- debian/tests/run-unit-test


Changes:

=====================================
debian/biobambam2-examples.install
=====================================
@@ -0,0 +1,3 @@
+debian/tests/data/*                 usr/share/doc/biobambam2/examples/
+debian/tests/data/README.test_data	usr/share/doc/biobambam2/
+debian/tests/run-unit-test		    usr/share/doc/biobambam2/


=====================================
debian/control
=====================================
@@ -16,8 +16,9 @@ Package: biobambam2
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends}
+Suggests: biobambam2-examples
 Description: tools for early stage alignment file processing
- This package contains some tools for processing BAM files including
+ This package contains some tools for processing BAM files, including
  .
    bamsormadup:  parallel sorting and duplicate marking
    bamcollate2:  reads BAM and writes BAM reordered such that alignment
@@ -32,3 +33,25 @@ Description: tools for early stage alignment file processing
                   query name
    bamtofastq:    reads BAM and writes FastQ; output can be collated
                   or uncollated by query name
+
+Package: biobambam2-examples
+Architecture: any
+Depends: ${misc:Depends}
+Enhances: biobambam2
+Description: tools for early stage alignment file processing
+ The biobambam2 package contains some tools for processing BAM files, including
+ .
+   bamsormadup:  parallel sorting and duplicate marking
+   bamcollate2:  reads BAM and writes BAM reordered such that alignment
+                 or collated by query name
+   bammarkduplicates: reads BAM and writes BAM with duplicate alignments
+                 marked using the BAM flags field
+   bammaskflags: reads BAM and writes BAM while masking (removing) bits
+                 from the flags column
+   bamrecompress: reads BAM and writes BAM with a defined compression
+                  setting. This tool is capable of multi-threading.
+   bamsort:       reads BAM and writes BAM resorted by coordinates or
+                  query name
+   bamtofastq:    reads BAM and writes FastQ; output can be collated
+                  or uncollated by query name
+   This package contains some examples that can be used for testing biobambam2.
\ No newline at end of file


=====================================
debian/docs
=====================================
@@ -1,5 +1,3 @@
 README
 README.md
 debian/README.test
-debian/tests/run-unit-test
-debian/tests/data/README.test-data


=====================================
debian/tests/run-unit-test
=====================================
@@ -42,7 +42,7 @@ echo -e "\e[92m\e[1mPassed\e[0m"
 echo
 
 echo -e "\e[93m\e[1mTest 6\e[0m"
-bamrecompress level=3 < SRR11728627.sam > SRR11728627.lvl3.bam
+bamrecompress level=9 < SRR11728627.bam > SRR11728627.lvl9.bam
 echo -e "\e[92m\e[1mPassed\e[0m"
 echo
 



View it on GitLab: https://salsa.debian.org/med-team/biobambam2/-/compare/fb026bc87d67fdb91dc848459d7c0334d2e7c539...8f789457d4b490ef2ec7174ccfbcaa8545413557

-- 
View it on GitLab: https://salsa.debian.org/med-team/biobambam2/-/compare/fb026bc87d67fdb91dc848459d7c0334d2e7c539...8f789457d4b490ef2ec7174ccfbcaa8545413557
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