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Feature/mm flag modifier #36

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15 commits merged into from
Mar 7, 2019
Merged

Feature/mm flag modifier #36

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e8a6b2c
Remove chmod and execute via bash command, also makes errors easier t…
keiranmraine Feb 20, 2019
ef03224
Fix deps in travis
keiranmraine Feb 20, 2019
400eb6f
More libs for bioperl
keiranmraine Feb 20, 2019
74c0320
Minor cleanup of TOC to force new commit ref for CI
keiranmraine Feb 21, 2019
cb2dea5
Version and changes
keiranmraine Feb 23, 2019
6351128
Initial commit of mismatch flag modifier
Mar 4, 2019
727bacf
Remove BAM_FDUP (dupicate flag) from mismatchQC bad flags list
Mar 7, 2019
b5b10e4
Update CHANGES.md
Mar 7, 2019
8d7ea50
Move destroy methods
Mar 7, 2019
17ba1a2
Add test files for mmFlagModifier
Mar 7, 2019
4d7d5c6
Merge in hotfix/4.2.7
Mar 7, 2019
61765fb
Minor update to CHANGES.md
Mar 7, 2019
17ef870
Add description of mmFlagModifier to
Mar 7, 2019
1f5329a
Add description of mmFlagModifier to
Mar 7, 2019
f3384ac
Modify example mmFlagModifier command
Mar 7, 2019
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Remove BAM_FDUP (dupicate flag) from mismatchQC bad flags list
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David Jones committed Mar 7, 2019
commit 727bacf407d519406365b3ec1bfb32919913f390
2 changes: 1 addition & 1 deletion c/mismatchQc.c
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Expand Up @@ -54,7 +54,7 @@ long long int marked_count = 0;
read fails platform/vendor quality checks,
read is PCR or optical duplicate
*/
const int BAD_FLAGS = BAM_FUNMAP | BAM_FMUNMAP | BAM_FQCFAIL | BAM_FDUP | BAM_FSECONDARY | BAM_FSUPPLEMENTARY;
const int BAD_FLAGS = BAM_FUNMAP | BAM_FMUNMAP | BAM_FQCFAIL | BAM_FSECONDARY | BAM_FSUPPLEMENTARY;

enum rw_opts {
W_CRAM = 1,
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