Added missing bcftools invocation to command line for region processing #110
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nicholas-owen
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Mar 17, 2022
* Update RELEASES.md (Illumina#87) * Updated RELASES.md and normalization.md (Illumina#109)
nicholas-owen
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Mar 17, 2022
* Documentation updates for 0.3.12 release (Illumina#110) * Update RELEASES.md (Illumina#87) * Updated RELASES.md and normalization.md (Illumina#109) * Merge doc changes from dev (Illumina#112) * Update RELEASES.md (Illumina#87) * Updated RELASES.md and normalization.md (Illumina#109) * Update more docs (Illumina#111) * Update happy.md * Cleaned up normalisation.md * Update happy.md * Created a new section for working with genome VCFs * Added description of --filter-nonref * Updated description of --convert-gvcf-xxxx options * Added note toward beginning of document calling attention to genome VCF section * Fixed broken links in TOC * Fixed inconsistent case in headings
nicholas-owen
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Mar 17, 2022
* fix bold GFM rendering Without a space between the *** and the : , Github won't render *** as bold. * typos? * Clarify that INFO.VQSLOD is required for --roc * Update read me with GCC/G++ 4.9.2+ requirement See Illumina#66 * Remove regex dependency + fix test error with gcc 7.3 * Fix Docker build * Update rtg-tools to work with new Java * Documentation updates for 0.3.12 release (Illumina#110) * Update RELEASES.md (Illumina#87) * Updated RELASES.md and normalization.md (Illumina#109) * Merge doc changes from dev (Illumina#112) * Update RELEASES.md (Illumina#87) * Updated RELASES.md and normalization.md (Illumina#109) * Update more docs (Illumina#111) * Update happy.md * Cleaned up normalisation.md * Update happy.md * Created a new section for working with genome VCFs * Added description of --filter-nonref * Updated description of --convert-gvcf-xxxx options * Added note toward beginning of document calling attention to genome VCF section * Fixed broken links in TOC * Fixed inconsistent case in headings * Resolved merge conflict * Remove seemingly-unused ENV command * Restore ENV DEBIAN_FRONTEND=noninteractive
nicholas-owen
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Mar 17, 2022
* fix bold GFM rendering Without a space between the *** and the : , Github won't render *** as bold. * typos? * Clarify that INFO.VQSLOD is required for --roc * Update read me with GCC/G++ 4.9.2+ requirement See Illumina#66 * Remove regex dependency + fix test error with gcc 7.3 * Fix Docker build * Update rtg-tools to work with new Java * Updated RELASES.md and normalization.md (Illumina#109) * Documentation updates for 0.3.12 release (Illumina#110) * Update RELEASES.md (Illumina#87) * Updated RELASES.md and normalization.md (Illumina#109) * Update more docs (Illumina#111) * Update happy.md * Cleaned up normalisation.md * Update happy.md * Created a new section for working with genome VCFs * Added description of --filter-nonref * Updated description of --convert-gvcf-xxxx options * Added note toward beginning of document calling attention to genome VCF section * Fixed broken links in TOC * Fixed inconsistent case in headings * Merge doc changes from dev (Illumina#112) * Update RELEASES.md (Illumina#87) * Updated RELASES.md and normalization.md (Illumina#109) * Update more docs (Illumina#111) * Update happy.md * Cleaned up normalisation.md * Update happy.md * Created a new section for working with genome VCFs * Added description of --filter-nonref * Updated description of --convert-gvcf-xxxx options * Added note toward beginning of document calling attention to genome VCF section * Fixed broken links in TOC * Fixed inconsistent case in headings * Remove tag (Illumina#113) * Documentation updates for 0.3.12 release (Illumina#110) * Update RELEASES.md (Illumina#87) * Updated RELASES.md and normalization.md (Illumina#109) * Merge doc changes from dev (Illumina#112) * Update RELEASES.md (Illumina#87) * Updated RELASES.md and normalization.md (Illumina#109) * Update more docs (Illumina#111) * Update happy.md * Cleaned up normalisation.md * Update happy.md * Created a new section for working with genome VCFs * Added description of --filter-nonref * Updated description of --convert-gvcf-xxxx options * Added note toward beginning of document calling attention to genome VCF section * Fixed broken links in TOC * Fixed inconsistent case in headings * Resolved merge conflict * Remove seemingly-unused ENV command * Restore ENV DEBIAN_FRONTEND=noninteractive
nicholas-owen
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Mar 17, 2022
* Updated RELASES.md and normalization.md (Illumina#109) * Update more docs (Illumina#111) * Update happy.md * Cleaned up normalisation.md * Update happy.md * Created a new section for working with genome VCFs * Added description of --filter-nonref * Updated description of --convert-gvcf-xxxx options * Added note toward beginning of document calling attention to genome VCF section * Fixed broken links in TOC * Fixed inconsistent case in headings * Remove tag (Illumina#113) * Documentation updates for 0.3.12 release (Illumina#110) * Update RELEASES.md (Illumina#87) * Updated RELASES.md and normalization.md (Illumina#109) * Merge doc changes from dev (Illumina#112) * Update RELEASES.md (Illumina#87) * Updated RELASES.md and normalization.md (Illumina#109) * Update more docs (Illumina#111) * Update happy.md * Cleaned up normalisation.md * Update happy.md * Created a new section for working with genome VCFs * Added description of --filter-nonref * Updated description of --convert-gvcf-xxxx options * Added note toward beginning of document calling attention to genome VCF section * Fixed broken links in TOC * Fixed inconsistent case in headings * Clean merge (Illumina#115) * fix bold GFM rendering Without a space between the *** and the : , Github won't render *** as bold. * typos? * Clarify that INFO.VQSLOD is required for --roc * Update read me with GCC/G++ 4.9.2+ requirement See Illumina#66 * Remove regex dependency + fix test error with gcc 7.3 * Fix Docker build * Update rtg-tools to work with new Java * Documentation updates for 0.3.12 release (Illumina#110) * Update RELEASES.md (Illumina#87) * Updated RELASES.md and normalization.md (Illumina#109) * Merge doc changes from dev (Illumina#112) * Update RELEASES.md (Illumina#87) * Updated RELASES.md and normalization.md (Illumina#109) * Update more docs (Illumina#111) * Update happy.md * Cleaned up normalisation.md * Update happy.md * Created a new section for working with genome VCFs * Added description of --filter-nonref * Updated description of --convert-gvcf-xxxx options * Added note toward beginning of document calling attention to genome VCF section * Fixed broken links in TOC * Fixed inconsistent case in headings * Resolved merge conflict * Remove seemingly-unused ENV command * Restore ENV DEBIAN_FRONTEND=noninteractive
nicholas-owen
pushed a commit
to nicholas-owen/hap.py
that referenced
this pull request
Mar 17, 2022
* Documentation updates for 0.3.12 release (Illumina#110) * Update RELEASES.md (Illumina#87) * Updated RELASES.md and normalization.md (Illumina#109) * Merge doc changes from dev (Illumina#112) * Update RELEASES.md (Illumina#87) * Updated RELASES.md and normalization.md (Illumina#109) * Update more docs (Illumina#111) * Update happy.md * Cleaned up normalisation.md * Update happy.md * Created a new section for working with genome VCFs * Added description of --filter-nonref * Updated description of --convert-gvcf-xxxx options * Added note toward beginning of document calling attention to genome VCF section * Fixed broken links in TOC * Fixed inconsistent case in headings * Fix unmergable typo directly in master (Illumina#119) This little space has caused no end of problems in getting these branches synced up. I'm hopeful that attacking it directly at the source may relieve the issues.
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